0s autopkgtest [19:37:11]: starting date and time: 2024-03-16 19:37:11+0000 0s autopkgtest [19:37:11]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [19:37:11]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.towidiki/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-base,src:curl,src:glib2.0,src:libpng1.6,src:libpsl,src:libtirpc,src:libxt,src:openssl,src:orthanc-python,src:readline,src:wp2latex --apt-upgrade r-cran-pscbs --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 curl/8.5.0-2ubuntu7 glib2.0/2.79.3-3ubuntu5 libpng1.6/1.6.43-3 libpsl/0.21.2-1.1 libtirpc/1.3.4+ds-1.1 libxt/1:1.2.1-1.2 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 readline/8.2-3.1 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-arm64-6.secgroup --name adt-noble-arm64-r-cran-pscbs-20240316-193711-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 221s autopkgtest [19:40:52]: testbed dpkg architecture: arm64 222s autopkgtest [19:40:53]: testbed apt version: 2.7.12 222s autopkgtest [19:40:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 224s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 225s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3657 kB] 226s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 226s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 227s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 227s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 227s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 227s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 227s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 227s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4013 kB] 227s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 227s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 227s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 241s Fetched 9065 kB in 6s (1398 kB/s) 242s Reading package lists... 252s Reading package lists... 253s Building dependency tree... 253s Reading state information... 255s Calculating upgrade... 257s The following packages will be REMOVED: 257s libglib2.0-0 libssl3 257s The following NEW packages will be installed: 257s libglib2.0-0t64 libssl3t64 xdg-user-dirs 257s The following packages have been kept back: 257s curl 257s The following packages will be upgraded: 257s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 257s 5 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 257s Need to get 4592 kB of archives. 257s After this operation, 211 kB of additional disk space will be used. 257s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 257s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 258s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 258s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 258s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 258s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 258s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 258s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 260s Fetched 4592 kB in 1s (4528 kB/s) 261s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75850 files and directories currently installed.) 261s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 261s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 261s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 261s udisks2 depends on libglib2.0-0 (>= 2.77.0). 261s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 261s python3-gi depends on libglib2.0-0 (>= 2.77.0). 261s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 261s netplan.io depends on libglib2.0-0 (>= 2.70.0). 261s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 261s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 261s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 261s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 261s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 261s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 261s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 261s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 261s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 261s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 261s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 261s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 261s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 261s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 261s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 261s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 261s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 261s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 261s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 261s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 261s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 261s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 261s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 261s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 261s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 261s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 261s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 261s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 261s fwupd depends on libglib2.0-0 (>= 2.79.0). 261s bolt depends on libglib2.0-0 (>= 2.56.0). 261s 261s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75850 files and directories currently installed.) 261s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 261s Selecting previously unselected package libglib2.0-0t64:arm64. 262s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75825 files and directories currently installed.) 262s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 262s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 262s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 262s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 262s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 262s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 263s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 263s wget depends on libssl3 (>= 3.0.0). 263s u-boot-tools depends on libssl3 (>= 3.0.0). 263s tnftp depends on libssl3 (>= 3.0.0). 263s tcpdump depends on libssl3 (>= 3.0.0). 263s systemd-resolved depends on libssl3 (>= 3.0.0). 263s systemd depends on libssl3 (>= 3.0.0). 263s sudo depends on libssl3 (>= 3.0.0). 263s sbsigntool depends on libssl3 (>= 3.0.0). 263s rsync depends on libssl3 (>= 3.0.0). 263s python3-cryptography depends on libssl3 (>= 3.0.0). 263s openssh-server depends on libssl3 (>= 3.0.10). 263s openssh-client depends on libssl3 (>= 3.0.10). 263s mtd-utils depends on libssl3 (>= 3.0.0). 263s mokutil depends on libssl3 (>= 3.0.0). 263s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 263s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 263s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 263s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 263s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 263s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 263s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 263s libnvme1 depends on libssl3 (>= 3.0.0). 263s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 263s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 263s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 263s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 263s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 263s kmod depends on libssl3 (>= 3.0.0). 263s dhcpcd-base depends on libssl3 (>= 3.0.0). 263s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 263s 263s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75850 files and directories currently installed.) 263s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 263s Selecting previously unselected package libssl3t64:arm64. 264s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75839 files and directories currently installed.) 264s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 264s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 264s Preparing to unpack .../libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 264s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 264s Preparing to unpack .../libtirpc-common_1.3.4+ds-1.1_all.deb ... 264s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 264s Preparing to unpack .../readline-common_8.2-3.1_all.deb ... 264s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 264s Selecting previously unselected package xdg-user-dirs. 264s Preparing to unpack .../xdg-user-dirs_0.18-1_arm64.deb ... 265s Unpacking xdg-user-dirs (0.18-1) ... 265s Setting up xdg-user-dirs (0.18-1) ... 265s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 265s Setting up libtirpc-common (1.3.4+ds-1.1) ... 265s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 265s No schema files found: doing nothing. 265s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 265s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 265s Setting up openssl (3.0.13-0ubuntu1) ... 265s Setting up readline-common (8.2-3.1) ... 265s Processing triggers for man-db (2.12.0-3) ... 267s Processing triggers for install-info (7.1-3) ... 268s Processing triggers for libc-bin (2.39-0ubuntu2) ... 269s Reading package lists... 270s Building dependency tree... 270s Reading state information... 272s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 273s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 273s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 273s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 273s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 280s Reading package lists... 281s Reading package lists... 281s Building dependency tree... 281s Reading state information... 283s Calculating upgrade... 285s The following packages have been kept back: 285s curl 285s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 285s Reading package lists... 286s Building dependency tree... 286s Reading state information... 289s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 296s autopkgtest [19:42:07]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 297s autopkgtest [19:42:08]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-pscbs 302s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-pscbs 0.66.0-2 (dsc) [2361 B] 302s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-pscbs 0.66.0-2 (tar) [3692 kB] 302s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-pscbs 0.66.0-2 (diff) [3744 B] 303s gpgv: Signature made Mon Nov 1 20:33:04 2021 UTC 303s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 303s gpgv: issuer "nilesh@debian.org" 303s gpgv: Can't check signature: No public key 303s dpkg-source: warning: cannot verify inline signature for ./r-cran-pscbs_0.66.0-2.dsc: no acceptable signature found 304s autopkgtest [19:42:15]: testing package r-cran-pscbs version 0.66.0-2 304s autopkgtest [19:42:15]: build not needed 307s autopkgtest [19:42:18]: test run-unit-test: preparing testbed 309s Reading package lists... 310s Building dependency tree... 310s Reading state information... 311s Starting pkgProblemResolver with broken count: 0 312s Starting 2 pkgProblemResolver with broken count: 0 312s Done 314s The following additional packages will be installed: 314s curl fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 314s fonts-font-awesome fonts-glyphicons-halflings fonts-mathjax 314s javascript-common libblas3 libcairo2 libcurl4t64 libdatrie1 libdeflate0 314s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 314s libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootstrap4 libjs-d3 314s libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables 314s libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-mathjax 314s libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify 314s libjs-sifter.js libjs-twitter-bootstrap-datepicker liblapack3 liblerc4 314s liblua5.4-0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 314s libpaper-utils libpaper1 libpixman-1-0 libpng16-16t64 libpsl5t64 314s libreadline8t64 libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 314s libtirpc3t64 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 314s libxrender1 libxss1 libxt6t64 littler node-bootstrap-sass node-html5shiv 314s node-normalize.css pandoc pandoc-data r-base-core r-bioc-aroma.light 314s r-bioc-biocgenerics r-bioc-dnacopy r-cran-acepack r-cran-backports 314s r-cran-base64enc r-cran-bslib r-cran-cachem r-cran-checkmate r-cran-chron 315s r-cran-cli r-cran-cluster r-cran-codetools r-cran-colorspace 315s r-cran-commonmark r-cran-cpp11 r-cran-crayon r-cran-data.table r-cran-deldir 315s r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi 315s r-cran-farver r-cran-fastmap r-cran-fontawesome r-cran-foreign 315s r-cran-formula r-cran-fs r-cran-future r-cran-generics r-cran-ggplot2 315s r-cran-globals r-cran-glue r-cran-gridextra r-cran-gtable r-cran-highr 315s r-cran-hmisc r-cran-htmltable r-cran-htmltools r-cran-htmlwidgets 315s r-cran-httpuv r-cran-interp r-cran-isoband r-cran-jpeg r-cran-jquerylib 315s r-cran-jsonlite r-cran-knitr r-cran-labeling r-cran-later r-cran-lattice 315s r-cran-latticeextra r-cran-lifecycle r-cran-listenv r-cran-littler 315s r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-memoise 315s r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-nnet 315s r-cran-parallelly r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-png 315s r-cran-promises r-cran-pscbs r-cran-purrr r-cran-r.cache r-cran-r.methodss3 315s r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer 315s r-cran-rcpp r-cran-rcppeigen r-cran-rlang r-cran-rmarkdown r-cran-rpart 315s r-cran-rstudioapi r-cran-sass r-cran-scales r-cran-shiny r-cran-sourcetools 315s r-cran-stringi r-cran-stringr r-cran-survival r-cran-tibble r-cran-tidyr 315s r-cran-tidyselect r-cran-tinytex r-cran-utf8 r-cran-vctrs r-cran-viridis 315s r-cran-viridislite r-cran-withr r-cran-xfun r-cran-xtable r-cran-yaml unzip 315s x11-common xdg-utils zip 315s Suggested packages: 315s apache2 | lighttpd | httpd libjs-jquery-ui-docs fonts-mathjax-extras 315s fonts-stix libjs-mathjax-doc tcl8.6 tk8.6 nodejs texlive-latex-recommended 315s texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context 315s wkhtmltopdf librsvg2-bin groff ghc php python ruby libjs-katex 315s citation-style-language-styles elpa-ess r-doc-info | r-doc-pdf r-mathlib 315s r-base-html r-cran-princurve r-bioc-biobase r-bioc-s4vectors r-bioc-iranges 315s r-bioc-genomicranges r-bioc-delayedarray r-bioc-biostrings r-bioc-rsamtools 315s r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-runit 315s r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shinyjs 315s r-cran-polyclip r-cran-covr r-cran-markdown r-cran-sp r-cran-scatterplot3d 315s r-cran-magick r-cran-sf r-cran-testthat r-cran-getopt r-cran-httr 315s r-cran-bit64 r-cran-dbi r-cran-formattable r-cran-nanotime 315s r-cran-palmerpenguins r-cran-units r-cran-vdiffr r-cran-roxygen2 315s r-cran-inline r-cran-bench r-cran-blob r-cran-brio r-cran-callr r-cran-here 315s r-cran-hms r-cran-pkgbuild r-cran-pkgload r-cran-plm r-cran-zoo 315s Recommended packages: 315s node-jquery r-recommended r-base-dev r-doc-html r-cran-curl r-cran-testthat 315s r-cran-thematic r-cran-fastmatch r-cran-devtools r-cran-tinytest 315s r-cran-callr r-cran-covr r-cran-mockery r-cran-processx r-cran-ps 315s r-cran-rprojroot r-cran-whoami r-cran-xml2 r-cran-bench r-cran-brio 315s r-cran-decor r-cran-desc r-cran-lobstr r-cran-progress r-cran-bit64 315s r-cran-bit r-cran-xts r-cran-nanotime r-cran-zoo r-cran-broom r-cran-dbi 315s r-cran-dbplyr r-cran-rmysql r-cran-rpostgresql r-cran-rsqlite 315s r-cran-unitizer r-cran-rsvg r-cran-spelling r-cran-rhpcblasctl r-cran-r.rsp 315s r-cran-markdown r-cran-pkgload r-cran-hexbin r-cran-mapproj r-cran-maps 315s r-cran-multcomp r-cran-profvis r-cran-quantreg r-cran-ragg r-cran-sf 315s r-cran-svglite r-cran-vdiffr r-cran-waldo r-cran-testit r-cran-cairo 315s r-cran-httr r-cran-formatr r-cran-gridsvg r-cran-magick r-cran-reticulate 315s r-cran-rgl r-cran-tikzdevice r-cran-webshot node-highlight.js r-cran-lintr 315s r-cran-tidyverse r-cran-r.devices r-cran-lubridate r-cran-usethis 315s r-cran-dygraphs r-cran-rsconnect r-cran-downlit r-cran-dichromat r-cran-hms 315s r-cran-mockr r-cran-formattable r-cran-readr r-cran-pkgdown r-cran-zeallot 315s r-cran-remotes r-cran-renv r-cran-runit libfile-mimeinfo-perl 315s libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils 315s The following packages will be REMOVED: 315s libcurl4 libpng16-16 libpsl5 libreadline8 libtirpc3 315s The following NEW packages will be installed: 315s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 315s fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings 315s fonts-mathjax javascript-common libblas3 libcairo2 libcurl4t64 libdatrie1 315s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 315s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 315s libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery 315s libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json 315s libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js 315s libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker liblapack3 315s liblerc4 liblua5.4-0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 315s libpaper-utils libpaper1 libpixman-1-0 libpng16-16t64 libpsl5t64 315s libreadline8t64 libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 315s libtirpc3t64 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 315s libxrender1 libxss1 libxt6t64 littler node-bootstrap-sass node-html5shiv 315s node-normalize.css pandoc pandoc-data r-base-core r-bioc-aroma.light 315s r-bioc-biocgenerics r-bioc-dnacopy r-cran-acepack r-cran-backports 315s r-cran-base64enc r-cran-bslib r-cran-cachem r-cran-checkmate r-cran-chron 315s r-cran-cli r-cran-cluster r-cran-codetools r-cran-colorspace 315s r-cran-commonmark r-cran-cpp11 r-cran-crayon r-cran-data.table r-cran-deldir 315s r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi 315s r-cran-farver r-cran-fastmap r-cran-fontawesome r-cran-foreign 315s r-cran-formula r-cran-fs r-cran-future r-cran-generics r-cran-ggplot2 315s r-cran-globals r-cran-glue r-cran-gridextra r-cran-gtable r-cran-highr 315s r-cran-hmisc r-cran-htmltable r-cran-htmltools r-cran-htmlwidgets 315s r-cran-httpuv r-cran-interp r-cran-isoband r-cran-jpeg r-cran-jquerylib 315s r-cran-jsonlite r-cran-knitr r-cran-labeling r-cran-later r-cran-lattice 315s r-cran-latticeextra r-cran-lifecycle r-cran-listenv r-cran-littler 315s r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-memoise 315s r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-nnet 315s r-cran-parallelly r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-png 315s r-cran-promises r-cran-pscbs r-cran-purrr r-cran-r.cache r-cran-r.methodss3 315s r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer 315s r-cran-rcpp r-cran-rcppeigen r-cran-rlang r-cran-rmarkdown r-cran-rpart 315s r-cran-rstudioapi r-cran-sass r-cran-scales r-cran-shiny r-cran-sourcetools 315s r-cran-stringi r-cran-stringr r-cran-survival r-cran-tibble r-cran-tidyr 315s r-cran-tidyselect r-cran-tinytex r-cran-utf8 r-cran-vctrs r-cran-viridis 315s r-cran-viridislite r-cran-withr r-cran-xfun r-cran-xtable r-cran-yaml unzip 315s x11-common xdg-utils zip 315s The following packages will be upgraded: 315s curl 316s 1 upgraded, 184 newly installed, 5 to remove and 0 not upgraded. 316s Need to get 163 MB/163 MB of archives. 316s After this operation, 513 MB of additional disk space will be used. 316s Get:1 /tmp/autopkgtest.H7uPRv/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [740 B] 316s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 316s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 316s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 316s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB] 316s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB] 316s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [83.5 kB] 316s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 316s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 317s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 317s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 317s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 317s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 317s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 317s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 317s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 javascript-common all 11+nmu1 [5936 B] 317s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 317s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 317s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 317s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 317s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 317s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 317s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 317s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 317s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 317s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 318s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 318s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 318s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 318s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 318s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 318s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 318s Get:33 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 318s Get:34 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-popper.js all 1.16.1+ds-6 [54.1 kB] 318s Get:35 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [537 kB] 318s Get:36 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-d3 all 3.5.17-4 [132 kB] 318s Get:37 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-es5-shim all 4.6.7-2 [39.8 kB] 318s Get:38 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 318s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 318s Get:40 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 318s Get:41 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB] 318s Get:42 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3712 B] 318s Get:43 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB] 318s Get:44 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 318s Get:45 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-json all 0~20221030+~1.0.8-1 [20.6 kB] 318s Get:46 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-prettify all 2015.12.04+dfsg-1.1 [39.3 kB] 318s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 318s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 318s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 liblua5.4-0 arm64 5.4.6-3 [158 kB] 318s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 318s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 318s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 318s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 318s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 318s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 318s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 318s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 318s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 318s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 318s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 318s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 318s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 318s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 318s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 318s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 319s Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [168 kB] 319s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 319s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 319s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 319s Get:70 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-core arm64 4.3.3-2build1 [26.8 MB] 320s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB] 320s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B] 320s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 node-bootstrap-sass all 3.4.3-2 [187 kB] 320s Get:74 http://ftpmaster.internal/ubuntu noble/universe arm64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 320s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 node-normalize.css all 8.0.1-5 [10.8 kB] 320s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 pandoc-data all 3.1.3-1 [92.4 kB] 320s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 pandoc arm64 3.1.3+ds-2 [27.7 MB] 323s Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-biocgenerics all 0.48.1-2 [595 kB] 323s Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r.methodss3 all 1.8.2-1 [84.0 kB] 323s Get:80 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r.oo all 1.26.0-1 [955 kB] 323s Get:81 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r.utils all 2.12.3-1 [1386 kB] 323s Get:82 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrixstats arm64 1.2.0-1 [475 kB] 323s Get:83 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-aroma.light all 3.32.0-1 [576 kB] 323s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-dnacopy arm64 1.76.0-1 [379 kB] 323s Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-acepack arm64 1.4.2-1 [60.5 kB] 323s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-backports arm64 1.4.1-1 [101 kB] 323s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-base64enc arm64 0.1-3-3 [27.4 kB] 323s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rlang arm64 1.1.3-1 [1663 kB] 324s Get:89 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fastmap arm64 1.1.1-1 [69.6 kB] 324s Get:90 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cachem arm64 1.0.8-1 [72.3 kB] 324s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-digest arm64 0.6.34-1 [182 kB] 324s Get:92 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ellipsis arm64 0.3.2-2 [35.5 kB] 324s Get:93 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-htmltools arm64 0.5.7-1 [369 kB] 324s Get:94 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.5 kB] 324s Get:95 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jsonlite arm64 1.8.8+dfsg-1 [441 kB] 324s Get:96 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cli arm64 3.6.2-1 [1377 kB] 324s Get:97 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-glue arm64 1.7.0-1 [154 kB] 324s Get:98 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 324s Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-memoise all 2.0.1-1 [53.9 kB] 324s Get:100 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mime arm64 0.12-1 [35.8 kB] 324s Get:101 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fs arm64 1.6.3+dfsg-1 [227 kB] 324s Get:102 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r6 all 2.5.1-1 [99.0 kB] 324s Get:103 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rappdirs arm64 0.3.3-1 [47.5 kB] 325s Get:104 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sass arm64 0.4.8+dfsg-1 [952 kB] 325s Get:105 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-bslib all 0.6.1+dfsg-1 [5138 kB] 326s Get:106 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-checkmate arm64 2.3.1-1 [711 kB] 326s Get:107 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-chron arm64 2.3-61-2 [186 kB] 326s Get:108 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cluster arm64 2.1.6-1 [552 kB] 326s Get:109 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-codetools all 0.2-19-1 [90.5 kB] 326s Get:110 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-colorspace arm64 2.1-0+dfsg-1 [1540 kB] 326s Get:111 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-commonmark arm64 1.9.1-1 [127 kB] 326s Get:112 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cpp11 all 0.4.7-1 [266 kB] 326s Get:113 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-crayon all 1.5.2-1 [164 kB] 326s Get:114 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-data.table arm64 1.14.10+dfsg-1 [1844 kB] 327s Get:115 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-deldir arm64 2.0-4-1 [270 kB] 327s Get:116 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB] 327s Get:117 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 327s Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB] 327s Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 327s Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 327s Get:121 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 327s Get:122 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 328s Get:123 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-2 [415 kB] 328s Get:124 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-withr all 2.5.0-1 [225 kB] 328s Get:125 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyselect arm64 1.2.0+dfsg-1 [218 kB] 328s Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-dplyr arm64 1.1.4-1 [1513 kB] 328s Get:127 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-evaluate all 0.23-1 [90.2 kB] 328s Get:128 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-farver arm64 2.1.1-1 [1336 kB] 328s Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fontawesome all 0.5.2-1 [1300 kB] 328s Get:130 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-foreign arm64 0.8.86-1 [240 kB] 328s Get:131 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-formula all 1.2-5-1 [158 kB] 328s Get:132 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-globals all 0.16.2-1 [117 kB] 328s Get:133 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-listenv all 0.9.1+dfsg-1 [112 kB] 328s Get:134 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-parallelly arm64 1.37.1-1 [364 kB] 328s Get:135 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-future all 1.33.1+dfsg-1 [634 kB] 328s Get:136 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 328s Get:137 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 328s Get:138 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB] 329s Get:139 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 329s Get:140 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 329s Get:141 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 329s Get:142 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 330s Get:143 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 330s Get:144 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-munsell all 0.5.0-2build1 [208 kB] 330s Get:145 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 330s Get:146 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB] 330s Get:147 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-scales all 1.3.0-1 [603 kB] 330s Get:148 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 331s Get:149 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gridextra all 2.3-3build1 [1024 kB] 331s Get:150 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xfun arm64 0.41+dfsg-1 [415 kB] 331s Get:151 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-highr all 0.10+dfsg-1 [38.3 kB] 331s Get:152 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-survival arm64 3.5-8-1 [6116 kB] 331s Get:153 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rpart arm64 4.1.23-1 [660 kB] 331s Get:154 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nnet arm64 7.3-19-2 [111 kB] 331s Get:155 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringi arm64 1.8.3-1 [869 kB] 331s Get:156 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 332s Get:157 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-yaml arm64 2.3.8-1 [107 kB] 332s Get:158 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 332s Get:159 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-knitr all 1.45+dfsg-1 [917 kB] 332s Get:160 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tinytex all 0.49-1 [141 kB] 332s Get:161 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-modernizr all 2.6.2+ds1-5 [48.3 kB] 332s Get:162 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 332s Get:163 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB] 332s Get:164 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-later arm64 1.3.2+dfsg-1 [120 kB] 332s Get:165 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-promises arm64 1.2.1+dfsg-1 [282 kB] 332s Get:166 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-httpuv arm64 1.6.14+dfsg-1 [496 kB] 332s Get:167 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xtable all 1:1.8-4-2 [689 kB] 332s Get:168 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sourcetools arm64 0.1.7-1-1 [47.2 kB] 332s Get:169 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB] 332s Get:170 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-shiny all 1.8.0+dfsg-1 [2762 kB] 332s Get:171 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rmarkdown all 2.25+dfsg-3 [1481 kB] 332s Get:172 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-htmlwidgets all 1.6.4+dfsg-1 [123 kB] 332s Get:173 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rstudioapi all 0.15.0-1 [277 kB] 332s Get:174 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-purrr arm64 1.0.2-1 [501 kB] 332s Get:175 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 332s Get:176 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-htmltable all 2.4.2-1 [381 kB] 333s Get:177 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-viridis all 0.6.5-1 [2770 kB] 333s Get:178 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-png arm64 0.1-8-1 [39.9 kB] 333s Get:179 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jpeg arm64 0.1-10-1 [30.8 kB] 333s Get:180 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcppeigen arm64 0.3.3.9.4-1 [1180 kB] 333s Get:181 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-interp arm64 1.1-6-1 [1433 kB] 333s Get:182 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-latticeextra all 0.6-30-1 [2198 kB] 333s Get:183 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-hmisc arm64 5.1-1-1 [3486 kB] 333s Get:184 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r.cache all 0.16.0-1 [113 kB] 333s Get:185 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pscbs all 0.66.0-2 [4345 kB] 336s Preconfiguring packages ... 336s Fetched 163 MB in 18s (9149 kB/s) 336s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 336s wget depends on libpsl5 (>= 0.16.0). 336s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 336s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 336s 337s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75866 files and directories currently installed.) 337s Removing libpsl5:arm64 (0.21.2-1build1) ... 337s Selecting previously unselected package libpsl5t64:arm64. 337s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75861 files and directories currently installed.) 337s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 337s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 337s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ... 337s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 337s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75867 files and directories currently installed.) 337s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ... 338s Selecting previously unselected package libcurl4t64:arm64. 338s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75862 files and directories currently installed.) 338s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 338s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 338s dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested: 338s libplymouth5:arm64 depends on libpng16-16 (>= 1.6.2). 338s libfreetype6:arm64 depends on libpng16-16 (>= 1.6.2-1). 338s 338s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75868 files and directories currently installed.) 338s Removing libpng16-16:arm64 (1.6.43-1) ... 338s Selecting previously unselected package libpng16-16t64:arm64. 338s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75858 files and directories currently installed.) 338s Preparing to unpack .../libpng16-16t64_1.6.43-3_arm64.deb ... 338s Unpacking libpng16-16t64:arm64 (1.6.43-3) ... 339s dpkg: libreadline8:arm64: dependency problems, but removing anyway as you requested: 339s parted depends on libreadline8 (>= 6.0). 339s libpython3.12-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 339s libpython3.11-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 339s gpgsm depends on libreadline8 (>= 6.0). 339s gpgconf depends on libreadline8 (>= 6.0). 339s gpg depends on libreadline8 (>= 6.0). 339s gawk depends on libreadline8 (>= 6.0). 339s fdisk depends on libreadline8 (>= 6.0). 339s 339s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75869 files and directories currently installed.) 339s Removing libreadline8:arm64 (8.2-3) ... 339s Selecting previously unselected package libreadline8t64:arm64. 339s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75857 files and directories currently installed.) 339s Preparing to unpack .../libreadline8t64_8.2-3.1_arm64.deb ... 340s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' 340s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' 340s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' 340s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' 340s Unpacking libreadline8t64:arm64 (8.2-3.1) ... 340s dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested: 340s lsof depends on libtirpc3 (>= 1.0.2). 340s libpython3.12-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 340s libpython3.11-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 340s libnsl2:arm64 depends on libtirpc3 (>= 1.0.2). 340s iproute2 depends on libtirpc3 (>= 1.0.2). 340s 340s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75877 files and directories currently installed.) 340s Removing libtirpc3:arm64 (1.3.4+ds-1build1) ... 340s Selecting previously unselected package libtirpc3t64:arm64. 340s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75871 files and directories currently installed.) 340s Preparing to unpack .../000-libtirpc3t64_1.3.4+ds-1.1_arm64.deb ... 340s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' 340s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' 340s Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 341s Selecting previously unselected package fonts-dejavu-mono. 341s Preparing to unpack .../001-fonts-dejavu-mono_2.37-8_all.deb ... 341s Unpacking fonts-dejavu-mono (2.37-8) ... 341s Selecting previously unselected package fonts-dejavu-core. 341s Preparing to unpack .../002-fonts-dejavu-core_2.37-8_all.deb ... 341s Unpacking fonts-dejavu-core (2.37-8) ... 341s Selecting previously unselected package fontconfig-config. 341s Preparing to unpack .../003-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 342s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 342s Selecting previously unselected package libfontconfig1:arm64. 342s Preparing to unpack .../004-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 342s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 342s Selecting previously unselected package fontconfig. 342s Preparing to unpack .../005-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 342s Unpacking fontconfig (2.15.0-1ubuntu1) ... 342s Selecting previously unselected package fonts-font-awesome. 342s Preparing to unpack .../006-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 342s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 343s Selecting previously unselected package fonts-glyphicons-halflings. 343s Preparing to unpack .../007-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 343s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 343s Selecting previously unselected package fonts-mathjax. 343s Preparing to unpack .../008-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 343s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 344s Selecting previously unselected package javascript-common. 344s Preparing to unpack .../009-javascript-common_11+nmu1_all.deb ... 344s Unpacking javascript-common (11+nmu1) ... 344s Selecting previously unselected package libblas3:arm64. 344s Preparing to unpack .../010-libblas3_3.12.0-3_arm64.deb ... 344s Unpacking libblas3:arm64 (3.12.0-3) ... 344s Selecting previously unselected package libpixman-1-0:arm64. 344s Preparing to unpack .../011-libpixman-1-0_0.42.2-1_arm64.deb ... 344s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 344s Selecting previously unselected package libxcb-render0:arm64. 344s Preparing to unpack .../012-libxcb-render0_1.15-1_arm64.deb ... 344s Unpacking libxcb-render0:arm64 (1.15-1) ... 345s Selecting previously unselected package libxcb-shm0:arm64. 345s Preparing to unpack .../013-libxcb-shm0_1.15-1_arm64.deb ... 345s Unpacking libxcb-shm0:arm64 (1.15-1) ... 345s Selecting previously unselected package libxrender1:arm64. 345s Preparing to unpack .../014-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 345s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 345s Selecting previously unselected package libcairo2:arm64. 345s Preparing to unpack .../015-libcairo2_1.18.0-1_arm64.deb ... 345s Unpacking libcairo2:arm64 (1.18.0-1) ... 345s Selecting previously unselected package libdatrie1:arm64. 345s Preparing to unpack .../016-libdatrie1_0.2.13-3_arm64.deb ... 345s Unpacking libdatrie1:arm64 (0.2.13-3) ... 345s Selecting previously unselected package libdeflate0:arm64. 345s Preparing to unpack .../017-libdeflate0_1.19-1_arm64.deb ... 345s Unpacking libdeflate0:arm64 (1.19-1) ... 345s Selecting previously unselected package libgfortran5:arm64. 345s Preparing to unpack .../018-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 345s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 345s Selecting previously unselected package libgomp1:arm64. 345s Preparing to unpack .../019-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 345s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 345s Selecting previously unselected package libgraphite2-3:arm64. 346s Preparing to unpack .../020-libgraphite2-3_1.3.14-2_arm64.deb ... 346s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 346s Selecting previously unselected package libharfbuzz0b:arm64. 346s Preparing to unpack .../021-libharfbuzz0b_8.3.0-2_arm64.deb ... 346s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 346s Selecting previously unselected package x11-common. 346s Preparing to unpack .../022-x11-common_1%3a7.7+23ubuntu2_all.deb ... 346s Unpacking x11-common (1:7.7+23ubuntu2) ... 347s Selecting previously unselected package libice6:arm64. 347s Preparing to unpack .../023-libice6_2%3a1.0.10-1build2_arm64.deb ... 347s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 347s Selecting previously unselected package libjpeg-turbo8:arm64. 347s Preparing to unpack .../024-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 347s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 347s Selecting previously unselected package libjpeg8:arm64. 347s Preparing to unpack .../025-libjpeg8_8c-2ubuntu11_arm64.deb ... 347s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 347s Selecting previously unselected package libjs-bootstrap. 347s Preparing to unpack .../026-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 347s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 347s Selecting previously unselected package libjs-popper.js. 347s 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libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 349s Selecting previously unselected package libjs-jquery-datatables. 349s Preparing to unpack .../033-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 349s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 350s Selecting previously unselected package libjs-sifter.js. 350s Preparing to unpack .../034-libjs-sifter.js_0.6.0+dfsg-3_all.deb ... 350s Unpacking libjs-sifter.js (0.6.0+dfsg-3) ... 350s Selecting previously unselected package libjs-microplugin.js. 350s Preparing to unpack .../035-libjs-microplugin.js_0.0.3+dfsg-1.1_all.deb ... 350s Unpacking libjs-microplugin.js (0.0.3+dfsg-1.1) ... 350s Selecting previously unselected package libjs-jquery-selectize.js. 350s Preparing to unpack .../036-libjs-jquery-selectize.js_0.12.6+dfsg-1.1_all.deb ... 350s Unpacking libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... 350s Selecting previously unselected package libjs-jquery-ui. 350s Preparing to unpack .../037-libjs-jquery-ui_1.13.2+dfsg-1_all.deb 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previously unselected package libthai-data. 352s Preparing to unpack .../043-libthai-data_0.1.29-2_all.deb ... 352s Unpacking libthai-data (0.1.29-2) ... 352s Selecting previously unselected package libthai0:arm64. 352s Preparing to unpack .../044-libthai0_0.1.29-2_arm64.deb ... 352s Unpacking libthai0:arm64 (0.1.29-2) ... 352s Selecting previously unselected package libpango-1.0-0:arm64. 352s Preparing to unpack .../045-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 352s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 352s Selecting previously unselected package libpangoft2-1.0-0:arm64. 352s Preparing to unpack .../046-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 352s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 352s Selecting previously unselected package libpangocairo-1.0-0:arm64. 352s Preparing to unpack .../047-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 352s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 353s Selecting previously unselected package libpaper1:arm64. 353s 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(2.1-6.1ubuntu1) ... 354s Selecting previously unselected package libwebp7:arm64. 354s Preparing to unpack .../054-libwebp7_1.3.2-0.4_arm64.deb ... 354s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 354s Selecting previously unselected package libtiff6:arm64. 354s Preparing to unpack .../055-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 354s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 355s Selecting previously unselected package libxft2:arm64. 355s Preparing to unpack .../056-libxft2_2.3.6-1_arm64.deb ... 355s Unpacking libxft2:arm64 (2.3.6-1) ... 355s Selecting previously unselected package libxss1:arm64. 355s Preparing to unpack .../057-libxss1_1%3a1.2.3-1build2_arm64.deb ... 355s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 355s Selecting previously unselected package libtk8.6:arm64. 355s Preparing to unpack .../058-libtk8.6_8.6.13-2_arm64.deb ... 355s Unpacking libtk8.6:arm64 (8.6.13-2) ... 355s Selecting previously unselected package libxt6t64:arm64. 355s Preparing to unpack .../059-libxt6t64_1%3a1.2.1-1.2_arm64.deb ... 355s Unpacking libxt6t64:arm64 (1:1.2.1-1.2) ... 355s Selecting previously unselected package zip. 355s Preparing to unpack .../060-zip_3.0-13_arm64.deb ... 355s Unpacking zip (3.0-13) ... 356s Selecting previously unselected package unzip. 356s Preparing to unpack .../061-unzip_6.0-28ubuntu3_arm64.deb ... 356s Unpacking unzip (6.0-28ubuntu3) ... 356s Selecting previously unselected package xdg-utils. 356s Preparing to unpack .../062-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 356s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 356s Selecting previously unselected package r-base-core. 356s Preparing to unpack .../063-r-base-core_4.3.3-2build1_arm64.deb ... 356s Unpacking r-base-core (4.3.3-2build1) ... 362s Selecting previously unselected package r-cran-littler. 362s Preparing to unpack .../064-r-cran-littler_0.3.19-1_arm64.deb ... 362s Unpacking r-cran-littler (0.3.19-1) ... 362s Selecting previously unselected package littler. 362s Preparing to unpack .../065-littler_0.3.19-1_all.deb ... 362s Unpacking littler (0.3.19-1) ... 362s Selecting previously unselected package node-bootstrap-sass. 362s Preparing to unpack .../066-node-bootstrap-sass_3.4.3-2_all.deb ... 362s Unpacking node-bootstrap-sass (3.4.3-2) ... 362s Selecting previously unselected package node-html5shiv. 362s Preparing to unpack .../067-node-html5shiv_3.7.3+dfsg-5_all.deb ... 362s Unpacking node-html5shiv (3.7.3+dfsg-5) ... 363s Selecting previously unselected package node-normalize.css. 363s Preparing to unpack .../068-node-normalize.css_8.0.1-5_all.deb ... 363s Unpacking node-normalize.css (8.0.1-5) ... 363s Selecting previously unselected package pandoc-data. 363s Preparing to unpack .../069-pandoc-data_3.1.3-1_all.deb ... 363s Unpacking pandoc-data (3.1.3-1) ... 363s Selecting previously unselected package pandoc. 363s Preparing to unpack .../070-pandoc_3.1.3+ds-2_arm64.deb ... 363s Unpacking pandoc (3.1.3+ds-2) ... 376s Selecting previously unselected package r-bioc-biocgenerics. 376s Preparing to unpack .../071-r-bioc-biocgenerics_0.48.1-2_all.deb ... 376s Unpacking r-bioc-biocgenerics (0.48.1-2) ... 376s Selecting previously unselected package r-cran-r.methodss3. 376s Preparing to unpack .../072-r-cran-r.methodss3_1.8.2-1_all.deb ... 376s Unpacking r-cran-r.methodss3 (1.8.2-1) ... 376s Selecting previously unselected package r-cran-r.oo. 376s Preparing to unpack .../073-r-cran-r.oo_1.26.0-1_all.deb ... 376s Unpacking r-cran-r.oo (1.26.0-1) ... 377s Selecting previously unselected package r-cran-r.utils. 377s Preparing to unpack .../074-r-cran-r.utils_2.12.3-1_all.deb ... 377s Unpacking r-cran-r.utils (2.12.3-1) ... 377s Selecting previously unselected package r-cran-matrixstats. 377s Preparing to unpack .../075-r-cran-matrixstats_1.2.0-1_arm64.deb ... 377s Unpacking r-cran-matrixstats (1.2.0-1) ... 378s Selecting previously unselected package r-bioc-aroma.light. 378s Preparing to unpack .../076-r-bioc-aroma.light_3.32.0-1_all.deb ... 378s Unpacking r-bioc-aroma.light (3.32.0-1) ... 378s Selecting previously unselected package r-bioc-dnacopy. 378s Preparing to unpack .../077-r-bioc-dnacopy_1.76.0-1_arm64.deb ... 378s Unpacking r-bioc-dnacopy (1.76.0-1) ... 378s Selecting previously unselected package r-cran-acepack. 378s Preparing to unpack .../078-r-cran-acepack_1.4.2-1_arm64.deb ... 378s Unpacking r-cran-acepack (1.4.2-1) ... 378s Selecting previously unselected package r-cran-backports. 378s Preparing to unpack .../079-r-cran-backports_1.4.1-1_arm64.deb ... 378s Unpacking r-cran-backports (1.4.1-1) ... 379s Selecting previously unselected package r-cran-base64enc. 379s Preparing to unpack .../080-r-cran-base64enc_0.1-3-3_arm64.deb ... 379s Unpacking r-cran-base64enc (0.1-3-3) ... 379s Selecting previously unselected package r-cran-rlang. 379s Preparing to unpack .../081-r-cran-rlang_1.1.3-1_arm64.deb ... 379s Unpacking r-cran-rlang (1.1.3-1) ... 379s Selecting previously unselected package r-cran-fastmap. 379s Preparing to unpack .../082-r-cran-fastmap_1.1.1-1_arm64.deb ... 379s Unpacking r-cran-fastmap (1.1.1-1) ... 379s Selecting previously unselected package r-cran-cachem. 379s Preparing to unpack .../083-r-cran-cachem_1.0.8-1_arm64.deb ... 379s Unpacking r-cran-cachem (1.0.8-1) ... 380s Selecting previously unselected package r-cran-digest. 380s Preparing to unpack .../084-r-cran-digest_0.6.34-1_arm64.deb ... 380s Unpacking r-cran-digest (0.6.34-1) ... 380s Selecting previously unselected package r-cran-ellipsis. 380s Preparing to unpack .../085-r-cran-ellipsis_0.3.2-2_arm64.deb ... 380s Unpacking r-cran-ellipsis (0.3.2-2) ... 380s Selecting previously unselected package r-cran-htmltools. 380s Preparing to unpack .../086-r-cran-htmltools_0.5.7-1_arm64.deb ... 380s Unpacking r-cran-htmltools (0.5.7-1) ... 380s Selecting previously unselected package r-cran-jquerylib. 380s Preparing to unpack .../087-r-cran-jquerylib_0.1.4+dfsg-4_all.deb ... 380s Unpacking r-cran-jquerylib (0.1.4+dfsg-4) ... 380s Selecting previously unselected package r-cran-jsonlite. 380s Preparing to unpack .../088-r-cran-jsonlite_1.8.8+dfsg-1_arm64.deb ... 380s Unpacking r-cran-jsonlite (1.8.8+dfsg-1) ... 381s Selecting previously unselected package r-cran-cli. 381s Preparing to unpack .../089-r-cran-cli_3.6.2-1_arm64.deb ... 381s Unpacking r-cran-cli (3.6.2-1) ... 382s Selecting previously unselected package r-cran-glue. 382s Preparing to unpack .../090-r-cran-glue_1.7.0-1_arm64.deb ... 382s Unpacking r-cran-glue (1.7.0-1) ... 383s Selecting previously unselected package r-cran-lifecycle. 383s Preparing to unpack .../091-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 383s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 383s Selecting previously unselected package r-cran-memoise. 383s Preparing to unpack .../092-r-cran-memoise_2.0.1-1_all.deb ... 383s Unpacking r-cran-memoise (2.0.1-1) ... 383s Selecting previously unselected package r-cran-mime. 383s Preparing to unpack .../093-r-cran-mime_0.12-1_arm64.deb ... 383s Unpacking r-cran-mime (0.12-1) ... 383s Selecting previously unselected package r-cran-fs. 384s Preparing to unpack .../094-r-cran-fs_1.6.3+dfsg-1_arm64.deb ... 384s Unpacking r-cran-fs (1.6.3+dfsg-1) ... 384s Selecting previously unselected package r-cran-r6. 384s Preparing to unpack .../095-r-cran-r6_2.5.1-1_all.deb ... 384s Unpacking r-cran-r6 (2.5.1-1) ... 384s Selecting previously unselected package r-cran-rappdirs. 384s Preparing to unpack .../096-r-cran-rappdirs_0.3.3-1_arm64.deb ... 384s Unpacking r-cran-rappdirs (0.3.3-1) ... 384s Selecting previously unselected package r-cran-sass. 384s Preparing to unpack .../097-r-cran-sass_0.4.8+dfsg-1_arm64.deb ... 384s Unpacking r-cran-sass (0.4.8+dfsg-1) ... 385s Selecting previously unselected package r-cran-bslib. 385s Preparing to unpack .../098-r-cran-bslib_0.6.1+dfsg-1_all.deb ... 385s Unpacking r-cran-bslib (0.6.1+dfsg-1) ... 386s Selecting previously unselected package r-cran-checkmate. 386s Preparing to unpack .../099-r-cran-checkmate_2.3.1-1_arm64.deb ... 386s Unpacking r-cran-checkmate (2.3.1-1) ... 386s Selecting previously unselected package r-cran-chron. 386s Preparing to unpack .../100-r-cran-chron_2.3-61-2_arm64.deb ... 386s Unpacking r-cran-chron (2.3-61-2) ... 387s Selecting previously unselected package r-cran-cluster. 387s Preparing to unpack .../101-r-cran-cluster_2.1.6-1_arm64.deb ... 387s Unpacking r-cran-cluster (2.1.6-1) ... 387s Selecting previously unselected package r-cran-codetools. 387s Preparing to unpack .../102-r-cran-codetools_0.2-19-1_all.deb ... 387s Unpacking r-cran-codetools (0.2-19-1) ... 387s Selecting previously unselected package r-cran-colorspace. 387s Preparing to unpack .../103-r-cran-colorspace_2.1-0+dfsg-1_arm64.deb ... 387s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ... 387s Selecting previously unselected package r-cran-commonmark. 387s Preparing to unpack .../104-r-cran-commonmark_1.9.1-1_arm64.deb ... 387s Unpacking r-cran-commonmark (1.9.1-1) ... 388s Selecting previously unselected package r-cran-cpp11. 388s Preparing to unpack .../105-r-cran-cpp11_0.4.7-1_all.deb ... 388s Unpacking r-cran-cpp11 (0.4.7-1) ... 388s Selecting previously unselected package r-cran-crayon. 388s Preparing to unpack .../106-r-cran-crayon_1.5.2-1_all.deb ... 388s Unpacking r-cran-crayon (1.5.2-1) ... 388s Selecting previously unselected package r-cran-data.table. 388s Preparing to unpack .../107-r-cran-data.table_1.14.10+dfsg-1_arm64.deb ... 388s Unpacking r-cran-data.table (1.14.10+dfsg-1) ... 389s Selecting previously unselected package r-cran-deldir. 389s Preparing to unpack .../108-r-cran-deldir_2.0-4-1_arm64.deb ... 389s Unpacking r-cran-deldir (2.0-4-1) ... 389s Selecting previously unselected package r-cran-generics. 389s Preparing to unpack .../109-r-cran-generics_0.1.3-1_all.deb ... 389s Unpacking r-cran-generics (0.1.3-1) ... 389s Selecting previously unselected package r-cran-magrittr. 389s Preparing to unpack .../110-r-cran-magrittr_2.0.3-1_arm64.deb ... 389s Unpacking r-cran-magrittr (2.0.3-1) ... 389s Selecting previously unselected package r-cran-fansi. 389s Preparing to unpack .../111-r-cran-fansi_1.0.5-1_arm64.deb ... 389s Unpacking r-cran-fansi (1.0.5-1) ... 390s Selecting previously unselected package r-cran-utf8. 390s Preparing to unpack .../112-r-cran-utf8_1.2.4-1_arm64.deb ... 390s Unpacking r-cran-utf8 (1.2.4-1) ... 390s Selecting previously unselected package r-cran-vctrs. 390s Preparing to unpack .../113-r-cran-vctrs_0.6.5-1_arm64.deb ... 390s Unpacking r-cran-vctrs (0.6.5-1) ... 390s Selecting previously unselected package r-cran-pillar. 390s Preparing to unpack .../114-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 390s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 391s Selecting previously unselected package r-cran-pkgconfig. 391s Preparing to unpack .../115-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 391s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 391s Selecting previously unselected package r-cran-tibble. 391s Preparing to unpack .../116-r-cran-tibble_3.2.1+dfsg-2_arm64.deb ... 391s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 392s Selecting previously unselected package r-cran-withr. 392s Preparing to unpack .../117-r-cran-withr_2.5.0-1_all.deb ... 392s Unpacking r-cran-withr (2.5.0-1) ... 392s Selecting previously unselected package r-cran-tidyselect. 392s Preparing to unpack .../118-r-cran-tidyselect_1.2.0+dfsg-1_arm64.deb ... 392s Unpacking r-cran-tidyselect (1.2.0+dfsg-1) ... 392s Selecting previously unselected package r-cran-dplyr. 392s Preparing to unpack .../119-r-cran-dplyr_1.1.4-1_arm64.deb ... 392s Unpacking r-cran-dplyr (1.1.4-1) ... 393s Selecting previously unselected package r-cran-evaluate. 393s Preparing to unpack .../120-r-cran-evaluate_0.23-1_all.deb ... 393s Unpacking r-cran-evaluate (0.23-1) ... 393s Selecting previously unselected package r-cran-farver. 393s Preparing to unpack .../121-r-cran-farver_2.1.1-1_arm64.deb ... 393s Unpacking r-cran-farver (2.1.1-1) ... 394s Selecting previously unselected package r-cran-fontawesome. 394s Preparing to unpack .../122-r-cran-fontawesome_0.5.2-1_all.deb ... 394s Unpacking r-cran-fontawesome (0.5.2-1) ... 394s Selecting previously unselected package r-cran-foreign. 394s Preparing to unpack .../123-r-cran-foreign_0.8.86-1_arm64.deb ... 394s Unpacking r-cran-foreign (0.8.86-1) ... 394s Selecting previously unselected package r-cran-formula. 394s Preparing to unpack .../124-r-cran-formula_1.2-5-1_all.deb ... 394s Unpacking r-cran-formula (1.2-5-1) ... 394s Selecting previously unselected package r-cran-globals. 394s Preparing to unpack .../125-r-cran-globals_0.16.2-1_all.deb ... 394s Unpacking r-cran-globals (0.16.2-1) ... 395s Selecting previously unselected package r-cran-listenv. 395s Preparing to unpack .../126-r-cran-listenv_0.9.1+dfsg-1_all.deb ... 395s Unpacking r-cran-listenv (0.9.1+dfsg-1) ... 395s Selecting previously unselected package r-cran-parallelly. 395s Preparing to unpack .../127-r-cran-parallelly_1.37.1-1_arm64.deb ... 395s Unpacking r-cran-parallelly (1.37.1-1) ... 396s Selecting previously unselected package r-cran-future. 396s Preparing to unpack .../128-r-cran-future_1.33.1+dfsg-1_all.deb ... 396s Unpacking r-cran-future (1.33.1+dfsg-1) ... 396s Selecting previously unselected package r-cran-gtable. 396s Preparing to unpack .../129-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 396s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 396s Selecting previously unselected package r-cran-isoband. 396s Preparing to unpack .../130-r-cran-isoband_0.2.7-1_arm64.deb ... 396s Unpacking r-cran-isoband (0.2.7-1) ... 396s Selecting previously unselected package r-cran-mass. 396s Preparing to unpack .../131-r-cran-mass_7.3-60.0.1-1_arm64.deb ... 396s Unpacking r-cran-mass (7.3-60.0.1-1) ... 396s Selecting previously unselected package r-cran-lattice. 397s Preparing to unpack .../132-r-cran-lattice_0.22-5-1_arm64.deb ... 397s Unpacking r-cran-lattice (0.22-5-1) ... 397s Selecting previously unselected package r-cran-nlme. 397s Preparing to unpack .../133-r-cran-nlme_3.1.164-1_arm64.deb ... 397s Unpacking r-cran-nlme (3.1.164-1) ... 397s Selecting previously unselected package r-cran-matrix. 397s Preparing to unpack .../134-r-cran-matrix_1.6-5-1_arm64.deb ... 397s Unpacking r-cran-matrix (1.6-5-1) ... 398s Selecting previously unselected package r-cran-mgcv. 398s Preparing to unpack .../135-r-cran-mgcv_1.9-1-1_arm64.deb ... 398s Unpacking r-cran-mgcv (1.9-1-1) ... 398s Selecting previously unselected package r-cran-labeling. 398s Preparing to unpack .../136-r-cran-labeling_0.4.3-1_all.deb ... 398s Unpacking r-cran-labeling (0.4.3-1) ... 398s Selecting previously unselected package r-cran-munsell. 398s Preparing to unpack .../137-r-cran-munsell_0.5.0-2build1_all.deb ... 398s Unpacking r-cran-munsell (0.5.0-2build1) ... 398s Selecting previously unselected package r-cran-rcolorbrewer. 398s Preparing to unpack .../138-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 398s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 398s Selecting previously unselected package r-cran-viridislite. 399s Preparing to unpack .../139-r-cran-viridislite_0.4.2-2_all.deb ... 399s Unpacking r-cran-viridislite (0.4.2-2) ... 399s Selecting previously unselected package r-cran-scales. 399s Preparing to unpack .../140-r-cran-scales_1.3.0-1_all.deb ... 399s Unpacking r-cran-scales (1.3.0-1) ... 399s Selecting previously unselected package r-cran-ggplot2. 399s Preparing to unpack .../141-r-cran-ggplot2_3.4.4+dfsg-1_all.deb ... 399s Unpacking r-cran-ggplot2 (3.4.4+dfsg-1) ... 400s Selecting previously unselected package r-cran-gridextra. 400s Preparing to unpack .../142-r-cran-gridextra_2.3-3build1_all.deb ... 400s Unpacking r-cran-gridextra (2.3-3build1) ... 400s Selecting previously unselected package r-cran-xfun. 400s Preparing to unpack .../143-r-cran-xfun_0.41+dfsg-1_arm64.deb ... 400s Unpacking r-cran-xfun (0.41+dfsg-1) ... 400s Selecting previously unselected package r-cran-highr. 400s Preparing to unpack .../144-r-cran-highr_0.10+dfsg-1_all.deb ... 400s Unpacking r-cran-highr (0.10+dfsg-1) ... 400s Selecting previously unselected package r-cran-survival. 400s Preparing to unpack .../145-r-cran-survival_3.5-8-1_arm64.deb ... 400s Unpacking r-cran-survival (3.5-8-1) ... 401s Selecting previously unselected package r-cran-rpart. 401s Preparing to unpack .../146-r-cran-rpart_4.1.23-1_arm64.deb ... 401s Unpacking r-cran-rpart (4.1.23-1) ... 401s Selecting previously unselected package r-cran-nnet. 401s Preparing to unpack .../147-r-cran-nnet_7.3-19-2_arm64.deb ... 401s Unpacking r-cran-nnet (7.3-19-2) ... 401s Selecting previously unselected package r-cran-stringi. 401s Preparing to unpack .../148-r-cran-stringi_1.8.3-1_arm64.deb ... 401s Unpacking r-cran-stringi (1.8.3-1) ... 401s Selecting previously unselected package r-cran-stringr. 401s Preparing to unpack .../149-r-cran-stringr_1.5.1-1_all.deb ... 401s Unpacking r-cran-stringr (1.5.1-1) ... 401s Selecting previously unselected package r-cran-yaml. 401s Preparing to unpack .../150-r-cran-yaml_2.3.8-1_arm64.deb ... 402s Unpacking r-cran-yaml (2.3.8-1) ... 402s Selecting previously unselected package libjs-mathjax. 402s Preparing to unpack .../151-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 402s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 411s Selecting previously unselected package r-cran-knitr. 411s Preparing to unpack .../152-r-cran-knitr_1.45+dfsg-1_all.deb ... 411s Unpacking r-cran-knitr (1.45+dfsg-1) ... 412s Selecting previously unselected package r-cran-tinytex. 412s Preparing to unpack .../153-r-cran-tinytex_0.49-1_all.deb ... 412s Unpacking r-cran-tinytex (0.49-1) ... 412s Selecting previously unselected package libjs-modernizr. 412s Preparing to unpack .../154-libjs-modernizr_2.6.2+ds1-5_all.deb ... 412s Unpacking libjs-modernizr (2.6.2+ds1-5) ... 412s Selecting previously unselected package r-cran-pkgkitten. 412s Preparing to unpack .../155-r-cran-pkgkitten_0.2.3-1_all.deb ... 412s Unpacking r-cran-pkgkitten (0.2.3-1) ... 412s Selecting previously unselected package r-cran-rcpp. 412s Preparing to unpack .../156-r-cran-rcpp_1.0.12-1_arm64.deb ... 412s Unpacking r-cran-rcpp (1.0.12-1) ... 413s Selecting previously unselected package r-cran-later. 413s Preparing to unpack .../157-r-cran-later_1.3.2+dfsg-1_arm64.deb ... 413s Unpacking r-cran-later (1.3.2+dfsg-1) ... 413s Selecting previously unselected package r-cran-promises. 414s Preparing to unpack .../158-r-cran-promises_1.2.1+dfsg-1_arm64.deb ... 414s Unpacking r-cran-promises (1.2.1+dfsg-1) ... 414s Selecting previously unselected package r-cran-httpuv. 414s Preparing to unpack .../159-r-cran-httpuv_1.6.14+dfsg-1_arm64.deb ... 414s Unpacking r-cran-httpuv (1.6.14+dfsg-1) ... 414s Selecting previously unselected package r-cran-xtable. 414s Preparing to unpack .../160-r-cran-xtable_1%3a1.8-4-2_all.deb ... 414s Unpacking r-cran-xtable (1:1.8-4-2) ... 414s Selecting previously unselected package r-cran-sourcetools. 414s Preparing to unpack .../161-r-cran-sourcetools_0.1.7-1-1_arm64.deb ... 414s Unpacking r-cran-sourcetools (0.1.7-1-1) ... 415s Selecting previously unselected package libjs-twitter-bootstrap-datepicker. 415s Preparing to unpack .../162-libjs-twitter-bootstrap-datepicker_1.3.1+dfsg1-4.1_all.deb ... 415s Unpacking libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... 415s Selecting previously unselected package r-cran-shiny. 415s Preparing to unpack .../163-r-cran-shiny_1.8.0+dfsg-1_all.deb ... 415s Unpacking r-cran-shiny (1.8.0+dfsg-1) ... 416s Selecting previously unselected package r-cran-rmarkdown. 416s Preparing to unpack .../164-r-cran-rmarkdown_2.25+dfsg-3_all.deb ... 416s Unpacking r-cran-rmarkdown (2.25+dfsg-3) ... 417s Selecting previously unselected package r-cran-htmlwidgets. 417s Preparing to unpack .../165-r-cran-htmlwidgets_1.6.4+dfsg-1_all.deb ... 417s Unpacking r-cran-htmlwidgets (1.6.4+dfsg-1) ... 417s Selecting previously unselected package r-cran-rstudioapi. 417s Preparing to unpack .../166-r-cran-rstudioapi_0.15.0-1_all.deb ... 417s Unpacking r-cran-rstudioapi (0.15.0-1) ... 418s Selecting previously unselected package r-cran-purrr. 418s Preparing to unpack .../167-r-cran-purrr_1.0.2-1_arm64.deb ... 418s Unpacking r-cran-purrr (1.0.2-1) ... 418s Selecting previously unselected package r-cran-tidyr. 418s Preparing to unpack .../168-r-cran-tidyr_1.3.1-1_arm64.deb ... 418s Unpacking r-cran-tidyr (1.3.1-1) ... 419s Selecting previously unselected package r-cran-htmltable. 419s Preparing to unpack .../169-r-cran-htmltable_2.4.2-1_all.deb ... 419s Unpacking r-cran-htmltable (2.4.2-1) ... 419s Selecting previously unselected package r-cran-viridis. 419s Preparing to unpack .../170-r-cran-viridis_0.6.5-1_all.deb ... 419s Unpacking r-cran-viridis (0.6.5-1) ... 420s Selecting previously unselected package r-cran-png. 420s Preparing to unpack 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up libxss1:arm64 (1:1.2.3-1build2) ... 433s Setting up libjs-bootstrap4 (4.6.1+dfsg1-4) ... 433s Setting up pandoc-data (3.1.3-1) ... 433s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 433s Setting up node-normalize.css (8.0.1-5) ... 433s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 433s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 433s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 433s Setting up libjs-bootstrap (3.4.1+dfsg-3) ... 433s Setting up libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... 433s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 433s Setting up libice6:arm64 (2:1.0.10-1build2) ... 433s Setting up liblapack3:arm64 (3.12.0-3) ... 433s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 433s Setting up libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 433s Setting up fontconfig-config 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... 438s 438s Creating config file /etc/R/Renviron with new version 439s Setting up r-cran-crayon (1.5.2-1) ... 439s Setting up r-cran-labeling (0.4.3-1) ... 439s Setting up r-cran-sourcetools (0.1.7-1-1) ... 439s Setting up r-cran-lattice (0.22-5-1) ... 439s Setting up r-cran-nlme (3.1.164-1) ... 439s Setting up r-cran-farver (2.1.1-1) ... 439s Setting up r-cran-formula (1.2-5-1) ... 439s Setting up r-cran-viridislite (0.4.2-2) ... 439s Setting up r-cran-cluster (2.1.6-1) ... 439s Setting up r-cran-nnet (7.3-19-2) ... 439s Setting up r-cran-commonmark (1.9.1-1) ... 439s Setting up r-cran-r6 (2.5.1-1) ... 439s Setting up r-cran-pkgkitten (0.2.3-1) ... 439s Setting up r-cran-jpeg (0.1-10-1) ... 439s Setting up r-cran-chron (2.3-61-2) ... 439s Setting up r-cran-magrittr (2.0.3-1) ... 439s Setting up r-cran-rappdirs (0.3.3-1) ... 439s Setting up r-cran-littler (0.3.19-1) ... 439s Setting up r-cran-fs (1.6.3+dfsg-1) ... 439s Setting up r-cran-rcpp (1.0.12-1) ... 439s Setting up r-cran-codetools (0.2-19-1) ... 439s Setting up r-bioc-biocgenerics (0.48.1-2) ... 439s Setting up r-cran-rlang (1.1.3-1) ... 439s Setting up r-cran-matrixstats (1.2.0-1) ... 439s Setting up r-cran-listenv (0.9.1+dfsg-1) ... 439s Setting up littler (0.3.19-1) ... 439s Setting up r-cran-xfun (0.41+dfsg-1) ... 439s Setting up r-cran-withr (2.5.0-1) ... 439s Setting up r-cran-backports (1.4.1-1) ... 439s Setting up r-cran-mime (0.12-1) ... 439s Setting up r-cran-generics (0.1.3-1) ... 439s Setting up r-cran-base64enc (0.1-3-3) ... 439s Setting up r-cran-digest (0.6.34-1) ... 439s Setting up r-cran-yaml (2.3.8-1) ... 439s Setting up r-cran-evaluate (0.23-1) ... 439s Setting up r-cran-highr (0.10+dfsg-1) ... 439s Setting up r-cran-fansi (1.0.5-1) ... 439s Setting up r-cran-mass (7.3-60.0.1-1) ... 439s Setting up r-cran-checkmate (2.3.1-1) ... 439s Setting up r-cran-acepack (1.4.2-1) ... 439s Setting up r-cran-data.table (1.14.10+dfsg-1) ... 439s Setting up r-cran-glue (1.7.0-1) ... 439s Setting up r-cran-foreign (0.8.86-1) ... 439s Setting up r-cran-xtable (1:1.8-4-2) ... 439s Setting up r-cran-cli (3.6.2-1) ... 439s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 439s Setting up r-cran-deldir (2.0-4-1) ... 439s Setting up r-cran-fastmap (1.1.1-1) ... 439s Setting up r-cran-png (0.1-8-1) ... 439s Setting up r-cran-r.methodss3 (1.8.2-1) ... 439s Setting up r-cran-jsonlite (1.8.8+dfsg-1) ... 439s Setting up r-cran-rstudioapi (0.15.0-1) ... 439s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 439s Setting up r-cran-utf8 (1.2.4-1) ... 439s Setting up r-cran-colorspace (2.1-0+dfsg-1) ... 439s Setting up r-cran-parallelly (1.37.1-1) ... 439s Setting up r-cran-stringi (1.8.3-1) ... 439s Setting up r-cran-cpp11 (0.4.7-1) ... 439s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 439s Setting up r-cran-isoband (0.2.7-1) ... 439s Setting up r-cran-gtable (0.3.4+dfsg-1) ... 439s Setting up r-cran-later (1.3.2+dfsg-1) ... 439s Setting up r-cran-matrix (1.6-5-1) ... 439s Setting up r-cran-tinytex (0.49-1) ... 439s Setting up r-cran-knitr (1.45+dfsg-1) ... 439s Setting up r-cran-mgcv (1.9-1-1) ... 439s Setting up r-bioc-dnacopy (1.76.0-1) ... 439s Setting up r-cran-cachem (1.0.8-1) ... 439s Setting up r-cran-globals (0.16.2-1) ... 439s Setting up r-cran-vctrs (0.6.5-1) ... 439s Setting up r-cran-rcppeigen (0.3.3.9.4-1) ... 439s Setting up r-cran-pillar (1.9.0+dfsg-1) ... 439s Setting up r-cran-ellipsis (0.3.2-2) ... 440s Setting up r-cran-stringr (1.5.1-1) ... 440s Setting up r-cran-munsell (0.5.0-2build1) ... 440s Setting up r-cran-tibble (3.2.1+dfsg-2) ... 440s Setting up r-cran-survival (3.5-8-1) ... 440s Setting up r-cran-r.oo (1.26.0-1) ... 440s Setting up r-cran-future (1.33.1+dfsg-1) ... 440s Setting up r-cran-tidyselect (1.2.0+dfsg-1) ... 440s Setting up r-cran-interp (1.1-6-1) ... 440s Setting up r-cran-gridextra (2.3-3build1) ... 440s Setting up r-cran-scales (1.3.0-1) ... 440s Setting up r-cran-memoise (2.0.1-1) ... 440s Setting up r-cran-promises (1.2.1+dfsg-1) ... 440s Setting up r-cran-purrr (1.0.2-1) ... 440s Setting up r-cran-htmltools (0.5.7-1) ... 440s Setting up r-cran-sass (0.4.8+dfsg-1) ... 440s Setting up r-cran-dplyr (1.1.4-1) ... 440s Setting up r-cran-r.utils (2.12.3-1) ... 440s Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ... 440s Setting up r-cran-httpuv (1.6.14+dfsg-1) ... 440s Setting up r-cran-rpart (4.1.23-1) ... 440s Setting up r-cran-fontawesome (0.5.2-1) ... 440s Setting up r-cran-latticeextra (0.6-30-1) ... 440s Setting up r-cran-jquerylib (0.1.4+dfsg-4) ... 440s Setting up r-cran-viridis (0.6.5-1) ... 440s Setting up r-cran-bslib (0.6.1+dfsg-1) ... 440s Setting up r-cran-tidyr (1.3.1-1) ... 440s Setting up r-bioc-aroma.light (3.32.0-1) ... 440s Setting up r-cran-r.cache (0.16.0-1) ... 440s Setting up r-cran-shiny (1.8.0+dfsg-1) ... 440s Setting up r-cran-pscbs (0.66.0-2) ... 440s Setting up r-cran-rmarkdown (2.25+dfsg-3) ... 440s Setting up r-cran-htmlwidgets (1.6.4+dfsg-1) ... 440s Setting up r-cran-htmltable (2.4.2-1) ... 440s Setting up r-cran-hmisc (5.1-1-1) ... 440s Setting up autopkgtest-satdep (0) ... 440s Processing triggers for man-db (2.12.0-3) ... 445s Processing triggers for install-info (7.1-3) ... 446s Processing triggers for libc-bin (2.39-0ubuntu2) ... 492s (Reading database ... 94904 files and directories currently installed.) 492s Removing autopkgtest-satdep (0) ... 494s autopkgtest [19:45:25]: test run-unit-test: [----------------------- 494s + pkg=r-cran-pscbs 494s + [ /tmp/autopkgtest.H7uPRv/autopkgtest_tmp = ] 494s + cd /tmp/autopkgtest.H7uPRv/autopkgtest_tmp 494s + cp -a /usr/share/doc/r-cran-pscbs/tests/PairedPSCBS,boot.R /usr/share/doc/r-cran-pscbs/tests/findLargeGaps.R /usr/share/doc/r-cran-pscbs/tests/randomSeed.R.gz /usr/share/doc/r-cran-pscbs/tests/segmentByCBS,calls.R /usr/share/doc/r-cran-pscbs/tests/segmentByCBS,futures.R /usr/share/doc/r-cran-pscbs/tests/segmentByCBS,median.R /usr/share/doc/r-cran-pscbs/tests/segmentByCBS,prune.R /usr/share/doc/r-cran-pscbs/tests/segmentByCBS,report.R /usr/share/doc/r-cran-pscbs/tests/segmentByCBS,shiftTCN.R /usr/share/doc/r-cran-pscbs/tests/segmentByCBS,weights.R.gz /usr/share/doc/r-cran-pscbs/tests/segmentByCBS.R.gz /usr/share/doc/r-cran-pscbs/tests/segmentByNonPairedPSCBS,medianDH.R /usr/share/doc/r-cran-pscbs/tests/segmentByPairedPSCBS,DH.R /usr/share/doc/r-cran-pscbs/tests/segmentByPairedPSCBS,calls.R /usr/share/doc/r-cran-pscbs/tests/segmentByPairedPSCBS,futures.R /usr/share/doc/r-cran-pscbs/tests/segmentByPairedPSCBS,noNormalBAFs.R /usr/share/doc/r-cran-pscbs/tests/segmentByPairedPSCBS,report.R /usr/share/doc/r-cran-pscbs/tests/segmentByPairedPSCBS,seqOfSegmentsByDP.R /usr/share/doc/r-cran-pscbs/tests/segmentByPairedPSCBS.R.gz /usr/share/doc/r-cran-pscbs/tests/weightedQuantile.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp 494s + find . -name *.gz -exec gunzip {} ; 494s + export LC_ALL=C 494s + dpkg-architecture -qDEB_HOST_ARCH 495s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 495s + hostarch=arm64 495s + [ arm64 = armhf ] 495s + + sedls s/\.R$// 495s PairedPSCBS,boot.R findLargeGaps.R randomSeed.R segmentByCBS,calls.R segmentByCBS,futures.R segmentByCBS,median.R segmentByCBS,prune.R segmentByCBS,report.R segmentByCBS,shiftTCN.R segmentByCBS,weights.R segmentByCBS.R segmentByNonPairedPSCBS,medianDH.R segmentByPairedPSCBS,DH.R segmentByPairedPSCBS,calls.R segmentByPairedPSCBS,futures.R segmentByPairedPSCBS,noNormalBAFs.R segmentByPairedPSCBS,report.R segmentByPairedPSCBS,seqOfSegmentsByDP.R segmentByPairedPSCBS.R weightedQuantile.R 495s + echo Begin test PairedPSCBS,boot 495s + exitcode=0 495s + R CMD BATCH PairedPSCBS,boot.R 495s Begin test PairedPSCBS,boot 513s + cat PairedPSCBS,boot.Rout 513s + [ 0 != 0 ] 513s + echo Test PairedPSCBS,boot passed 513s + echo 0 513s + echo Begin test findLargeGaps 513s + exitcode=0 513s + R CMD BATCH findLargeGaps.R 513s 513s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 513s Copyright (C) 2024 The R Foundation for Statistical Computing 513s Platform: aarch64-unknown-linux-gnu (64-bit) 513s 513s R is free software and comes with ABSOLUTELY NO WARRANTY. 513s You are welcome to redistribute it under certain conditions. 513s Type 'license()' or 'licence()' for distribution details. 513s 513s R is a collaborative project with many contributors. 513s Type 'contributors()' for more information and 513s 'citation()' on how to cite R or R packages in publications. 513s 513s Type 'demo()' for some demos, 'help()' for on-line help, or 513s 'help.start()' for an HTML browser interface to help. 513s Type 'q()' to quit R. 513s 513s > ########################################################### 513s > # This tests: 513s > # - Bootstrapping for PairedPSCBS objects 513s > ########################################################### 513s > library("PSCBS") 513s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 513s 513s Attaching package: 'PSCBS' 513s 513s The following objects are masked from 'package:base': 513s 513s append, load 513s 513s > 513s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 513s > # Load SNP microarray data 513s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 513s > data <- PSCBS::exampleData("paired.chr01") 513s > 513s > 513s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 513s > # Paired PSCBS segmentation 513s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 513s > # Drop single-locus outliers 513s > dataS <- dropSegmentationOutliers(data) 513s > dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 513s > nSegs <- 4L 513s > str(dataS) 513s 'data.frame': 14670 obs. of 6 variables: 513s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 513s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 513s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 513s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 513s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 513s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 513s > # Segment known regions 513s > knownSegments <- data.frame( 513s + chromosome = c( 1, 1, 1), 513s + start = c( -Inf, NA, 141510003), 513s + end = c(120992603, NA, +Inf) 513s + ) 513s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, avgDH="median", seed=0xBEEF) 513s > print(fit) 513s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 513s 1 1 1 1 554484 120992603 7586 1.385258 2108 513s 2 NA 2 1 NA NA NA NA 0 513s 3 1 3 1 141510003 185449813 2681 2.068861 777 513s 4 1 4 1 185449813 247137334 4391 2.634110 1311 513s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 513s 1 2108 2108 0.54551245 0.3147912 1.070467 513s 2 0 0 NA NA NA 513s 3 777 777 0.07132277 0.9606521 1.108209 513s 4 1311 1311 0.21663871 1.0317300 1.602380 513s > 513s > 513s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 513s > # Bootstrap 513s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 513s > B <- 1L 513s > seed <- 0xBEEF 513s > probs <- c(0.025, 0.05, 0.95, 0.975) 513s > 513s > sets <- getBootstrapLocusSets(fit, B=B, seed=seed) 513s > 513s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 513s > # Subset by first segment 513s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 513s > ss <- 1L 513s > 513s > fitT <- extractSegment(fit, ss) 513s > dataT <- getLocusData(fitT) 513s > segsT <- getSegments(fitT) 513s > 513s > # Truth 513s > bootT <- bootstrapSegmentsAndChangepoints(fitT, B=B, seed=seed) 513s > bootT1 <- bootT$segments[1L,,,drop=FALSE] 513s > types <- dimnames(bootT1)[[3L]] 513s > dim(bootT1) <- dim(bootT1)[-1L] 513s > colnames(bootT1) <- types 513s > sumsT <- apply(bootT1, MARGIN=2L, FUN=quantile, probs=probs) 513s > print(sumsT) 513s tcn dh c1 c2 513s 2.5% 1.383213 0.5466788 0.3135198 1.069693 513s 5% 1.383213 0.5466788 0.3135198 1.069693 513s 95% 1.383213 0.5466788 0.3135198 1.069693 513s 97.5% 1.383213 0.5466788 0.3135198 1.069693 513s > 513s > fitTB <- bootstrapTCNandDHByRegion(fitT, B=B, seed=seed) 513s > segsTB <- getSegments(fitTB) 513s > segsTB <- unlist(segsTB[,grep("_", colnames(segsTB))]) 513s > dim(segsTB) <- dim(sumsT) 513s > dimnames(segsTB) <- dimnames(sumsT) 513s > print(segsTB) 513s tcn dh c1 c2 513s 2.5% 1.383213 0.5466788 0.3135198 1.069693 513s 5% 1.383213 0.5466788 0.3135198 1.069693 513s 95% 1.383213 0.5466788 0.3135198 1.069693 513s 97.5% 1.383213 0.5466788 0.3135198 1.069693 513s > 513s > # Sanity check 513s > stopifnot(all.equal(segsTB, sumsT)) 513s > 513s > # Calculate summaries using the existing bootstrap samples 513s > fitTBp <- bootstrapTCNandDHByRegion(fitT, .boot=bootT) 513s > # Sanity check 513s > all.equal(fitTBp, fitTB) 513s [1] "Component \"tcn_2.5%\": Mean relative difference: 0.003070405" 513s [2] "Component \"tcn_5%\": Mean relative difference: 0.002241362" 513s [3] "Component \"tcn_95%\": Mean relative difference: 0.005458479" 513s [4] "Component \"tcn_97.5%\": Mean relative difference: 0.006030363" 513s [5] "Component \"dh_2.5%\": Mean relative difference: 0.02683423" 513s [6] "Component \"dh_5%\": Mean relative difference: 0.02409533" 513s [7] "Component \"dh_95%\": Mean relative difference: 0.0150081" 513s [8] "Component \"dh_97.5%\": Mean relative difference: 0.01826461" 513s [9] "Component \"c1_2.5%\": Mean relative difference: 0.02397349" 513s [10] "Component \"c1_5%\": Mean relative difference: 0.01800948" 513s [11] "Component \"c1_95%\": Mean relative difference: 0.0303456" 513s [12] "Component \"c1_97.5%\": Mean relative difference: 0.03420614" 513s [13] "Component \"c2_2.5%\": Mean relative difference: 0.008723378" 513s [14] "Component \"c2_5%\": Mean relative difference: 0.006834962" 513s [15] "Component \"c2_95%\": Mean relative difference: 0.00741949" 513s [16] "Component \"c2_97.5%\": Mean relative difference: 0.008743911" 513s attr(,"what") 513s [1] "getSegments()" 513s > 513s > 513s > # Bootstrap from scratch 513s > setsT <- getBootstrapLocusSets(fitT, B=B, seed=seed) 513s > lociT <- setsT$locusSet[[1L]]$bootstrap$loci 513s > idxs <- lociT$tcn 513s > tcnT <- array(dataT$CT[idxs], dim=dim(idxs)) 513s > tcnT <- apply(tcnT, MARGIN=2L, FUN=mean, na.rm=TRUE) 513s > idxs <- lociT$dh 513s > dhT <- array(dataT$rho[idxs], dim=dim(idxs)) 513s > dhT <- apply(dhT, MARGIN=2L, FUN=median, na.rm=TRUE) 513s > c1T <- (1-dhT) * tcnT / 2 513s > c2T <- tcnT - c1T 513s > bootT2 <- array(c(tcnT, dhT, c1T, c2T), dim=c(1L, 4L)) 513s > colnames(bootT2) <- colnames(bootT1) 513s > print(bootT2) 513s tcn dh c1 c2 513s [1,] 1.383213 0.5466788 0.3135198 1.069693 513s > 513s > # This comparison is only valid if B == 1L 513s > if (B == 1L) { 513s + # Sanity check 513s + stopifnot(all.equal(bootT2, bootT1)) 513s + } 513s > 513s > proc.time() 513s user system elapsed 513s 15.752 0.988 16.804 513s Test PairedPSCBS,boot passed 513s 0 513s Begin test findLargeGaps 517s + cat findLargeGaps.Rout 517s 517s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 517s Copyright (C) 2024 The R Foundation for Statistical Computing 517s Platform: aarch64-unknown-linux-gnu (64-bit) 517s 517s R is free software and comes with ABSOLUTELY NO WARRANTY. 517s You are welcome to redistribute it under certain conditions. 517s Type 'license()' or 'licence()' for distribution details. 517s 517s R is a collaborative project with many contributors. 517s Type 'contributors()' for more information and 517s 'citation()' on how to cite R or R packages in publications. 517s 517s Type 'demo()' for some demos, 'help()' for on-line help, or 517s 'help.start()' for an HTML browser interface to help. 517s Type 'q()' to quit R. 517s 517s [Previously saved workspace restored] 517s 517s > library("PSCBS") 517s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 517s 517s Attaching package: 'PSCBS' 517s 517s The following objects are masked from 'package:base': 517s 517s append, load 517s 517s > 517s > # Simulating copy-number data 517s > set.seed(0xBEEF) 517s > 517s > # Simulate CN data 517s > J <- 1000 517s > mu <- double(J) 517s > mu[200:300] <- mu[200:300] + 1 517s > mu[350:400] <- NA # centromere 517s > mu[650:800] <- mu[650:800] - 1 517s > eps <- rnorm(J, sd=1/2) 517s > y <- mu + eps 517s > x <- seq(from=1, to=100e6, length.out=J) 517s > 517s > data <- data.frame(chromosome=0L, x=x) 517s > 517s > gaps <- findLargeGaps(x=x, minLength=1e6) 517s > print(gaps) 517s [1] start end length 517s <0 rows> (or 0-length row.names) 517s > stopifnot(is.data.frame(gaps)) 517s > stopifnot(nrow(gaps) == 0L) 517s > segs <- gapsToSegments(gaps) 517s > print(segs) 517s chromosome start end 517s 1 0 -Inf Inf 517s > stopifnot(is.data.frame(segs)) 517s > stopifnot(nrow(segs) == 1L) 517s > 517s > 517s > gaps <- findLargeGaps(data, minLength=1e6) 517s > print(gaps) 517s [1] chromosome start end 517s <0 rows> (or 0-length row.names) 517s > stopifnot(is.data.frame(gaps)) 517s > stopifnot(nrow(gaps) == 0L) 517s > segs <- gapsToSegments(gaps) 517s > print(segs) 517s chromosome start end 517s 1 0 -Inf Inf 517s > stopifnot(is.data.frame(segs)) 517s > stopifnot(nrow(segs) == 1L) 517s > 517s > 517s > ## Add missing values 517s > data2 <- data 517s > data$x[30e6 < x & x < 50e6] <- NA 517s > gaps <- findLargeGaps(data, minLength=1e6) 517s > print(gaps) 517s chromosome start end length 517s 1 0 29929932 50050050 20120118 517s > stopifnot(is.data.frame(gaps)) 517s > stopifnot(nrow(gaps) == 1L) 517s > segs <- gapsToSegments(gaps) 517s > print(segs) 517s chromosome start end length 517s 1 0 -Inf 29929931 Inf 517s 2 0 29929932 50050050 20120118 517s 3 0 50050051 Inf Inf 517s > stopifnot(is.data.frame(segs)) 517s > stopifnot(nrow(segs) == 3L) 517s > 517s > 517s > 517s > # BUG FIX: Issue #6 517s > gaps <- findLargeGaps(chromosome=rep(1,10), x=1:10, minLength=2) 517s > print(gaps) 517s [1] chromosome start end 517s <0 rows> (or 0-length row.names) 517s > stopifnot(is.data.frame(gaps)) 517s > stopifnot(nrow(gaps) == 0L) 517s > # BUG FIX: Issue #9 517s > segs <- gapsToSegments(gaps) 517s > print(segs) 517s chromosome start end 517s 1 0 -Inf Inf 517s > stopifnot(is.data.frame(segs)) 517s > stopifnot(nrow(segs) == 1L) 517s > 517s > 517s > # BUG FIX: PSCBS GitHub Issue #8 517s > gaps <- try({ 517s + findLargeGaps(chromosome=rep(1,3), x=as.numeric(1:3), minLength=1) 517s + }) 517s Error in findLargeGaps.default(chromosome = rep(1, 3), x = as.numeric(1:3), : 517s Cannot identify large gaps. Argument 'resolution' (=1) is not strictly smaller than 'minLength' (=1). 517s > stopifnot(inherits(gaps, "try-error")) 517s > 517s > proc.time() 517s user system elapsed 517s 2.019 0.358 2.328 517s Test findLargeGaps passed 517s + [ 0 != 0 ] 517s + echo Test findLargeGaps passed 517s 0 517s Begin test randomSeed 517s + echo 0 517s + echo Begin test randomSeed 517s + exitcode=0 517s + R CMD BATCH randomSeed.R 520s + cat randomSeed.Rout 520s 520s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 520s Copyright (C) 2024 The R Foundation for Statistical Computing 520s Platform: aarch64-unknown-linux-gnu (64-bit) 520s 520s R is free software and comes with ABSOLUTELY NO WARRANTY. 520s You are welcome to redistribute it under certain conditions. 520s Type 'license()' or 'licence()' for distribution details. 520s 520s R is a collaborative project with many contributors. 520s Type 'contributors()' for more information and 520s 'citation()' on how to cite R or R packages in publications. 520s 520s Type 'demo()' for some demos, 'help()' for on-line help, or 520s 'help.start()' for an HTML browser interface to help. 520s Type 'q()' to quit R. 520s 520s [Previously saved workspace restored] 520s 520s > library("PSCBS") 520s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 520s 520s Attaching package: 'PSCBS' 520s 520s The following objects are masked from 'package:base': 520s 520s append, load 520s 520s > 520s > message("*** randomSeed() - setup ...") 520s *** randomSeed() - setup ... 520s > ovars <- ls(envir=globalenv()) 520s > genv <- globalenv() 520s > RNGkind("Mersenne-Twister") 520s > if (exists(".Random.seed", envir=genv, inherits=FALSE)) 520s + rm(list=".Random.seed", envir=genv, inherits=FALSE) 520s > seed0 <- genv$.Random.seed 520s > stopifnot(is.null(seed0)) 520s > okind0 <- RNGkind()[1L] 520s > 520s > sample1 <- function() { sample(0:9, size=1L) } 520s > message("*** randomSeed() - setup ... done") 520s *** randomSeed() - setup ... done 520s > 520s > 520s > message("*** randomSeed('get') ...") 520s *** randomSeed('get') ... 520s > ## Get random seed 520s > seed <- randomSeed("get") 520s > stopifnot(identical(seed, seed0)) 520s > 520s > ## Repeat after new sample 520s > y1 <- sample1() 520s > message(sprintf("Random number: %d", y1)) 520s Random number: 1 520s > seed1 <- randomSeed("get") 520s > stopifnot(!identical(seed1, seed0)) 520s > message("*** randomSeed('get') ... done") 520s *** randomSeed('get') ... done 520s > 520s > 520s > message("*** randomSeed('set', 42L) ...") 520s *** randomSeed('set', 42L) ... 520s > randomSeed("set", seed=42L) 520s > seed2 <- randomSeed("get") 520s > stopifnot(!identical(seed2, seed1)) 520s > 520s > y2 <- sample1() 520s > message(sprintf("Random number: %d (with random seed = 42L)", y2)) 520s Random number: 0 (with random seed = 42L) 520s > 520s > ## Reset to previous state 520s > randomSeed("reset") 520s > seed3 <- randomSeed("get") 520s > stopifnot(identical(seed3, seed1)) 520s > stopifnot(identical(RNGkind()[1L], okind0), 520s + identical(randomSeed("get"), seed1)) 520s > message("*** randomSeed('set', 42L) ... done") 520s *** randomSeed('set', 42L) ... done 520s > 520s > 520s > message("*** randomSeed('set', NULL) ...") 520s *** randomSeed('set', NULL) ... 520s > randomSeed("set", seed=NULL) 520s > seed4 <- randomSeed("get") 520s > stopifnot(is.null(seed4)) 520s > 520s > y3 <- sample1() 520s > message(sprintf("Random number: %d", y3)) 520s Random number: 8 520s > 520s > message("*** randomSeed('set', NULL) ... done") 520s *** randomSeed('set', NULL) ... done 520s > 520s > 520s > message("*** randomSeed('set', 42L) again ...") 520s *** randomSeed('set', 42L) again ... 520s > seed5 <- randomSeed("get") 520s > randomSeed("set", seed=42L) 520s > y4 <- sample1() 520s > message(sprintf("Random number: %d (with random seed = 42L)", y4)) 520s Random number: 0 (with random seed = 42L) 520s > stopifnot(identical(y4, y2)) 520s > 520s > randomSeed("reset") 520s > stopifnot(identical(RNGkind()[1L], okind0), 520s + identical(randomSeed("get"), seed5)) 520s > message("*** randomSeed('set', 42L) again ... done") 520s *** randomSeed('set', 42L) again ... done 520s > 520s > 520s > 520s > ## L'Ecuyer-CMRG: Random number generation for parallel processing 520s > message("*** randomSeed(): L'Ecuyer-CMRG stream ...") 520s *** randomSeed(): L'Ecuyer-CMRG stream ... 520s > 520s > okind <- RNGkind()[1L] 520s > stopifnot(identical(okind, okind0)) 520s > 520s > randomSeed("set", seed=NULL) 520s > oseed <- randomSeed("get") 520s > stopifnot(is.null(oseed)) 520s > 520s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 520s > oseed2 <- randomSeed("reset") 520s > str(oseed2) 520s NULL 520s > stopifnot(identical(oseed2, oseed)) 520s > stopifnot(identical(RNGkind()[1L], okind), 520s + identical(randomSeed("get"), oseed)) 520s > 520s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 520s > seed0 <- randomSeed("get") 520s > seeds0 <- lapply(1:10, FUN=function(i) randomSeed("advance")) 520s > oseed2 <- randomSeed("reset") 520s > stopifnot(identical(oseed2, oseed)) 520s > stopifnot(identical(RNGkind()[1L], okind), 520s + identical(randomSeed("get"), oseed)) 520s > 520s > 520s > ## Assert reproducible .Random.seed stream 520s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 520s > seed1 <- randomSeed("get") 520s > seeds1 <- lapply(1:10, FUN=function(i) randomSeed("advance")) 520s > stopifnot(identical(seed1, seed0)) 520s > stopifnot(identical(seeds1, seeds0)) 520s > 520s > randomSeed("reset") 520s > stopifnot(identical(RNGkind()[1L], okind), 520s + identical(randomSeed("get"), oseed)) 520s > 520s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 520s > seeds2 <- randomSeed("advance", n=10L) 520s > stopifnot(identical(seeds2, seeds0)) 520s > 520s > randomSeed("reset") 520s > stopifnot(identical(RNGkind()[1L], okind), 520s + identical(randomSeed("get"), oseed)) 520s > 520s > randomSeed("set", seed=seeds2[[1]], kind="L'Ecuyer-CMRG") 520s > randomSeed("reset") 520s > stopifnot(identical(RNGkind()[1L], okind), 520s + identical(randomSeed("get"), oseed)) 520s > 520s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 520s > y0 <- sapply(1:10, FUN=function(ii) { 520s + randomSeed("advance") 520s + sample1() 520s + }) 520s > print(y0) 520s [1] 6 9 6 9 9 9 0 7 6 5 520s > randomSeed("reset") 520s > 520s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 520s > y1 <- sapply(1:10, FUN=function(ii) { 520s + randomSeed("advance") 520s + sample1() 520s + }) 520s > print(y1) 520s [1] 6 9 6 9 9 9 0 7 6 5 520s > stopifnot(identical(y1, y0)) 520s > randomSeed("reset") 520s > 520s > stopifnot(identical(RNGkind()[1L], okind)) 520s > 520s > message("*** randomSeed(): L'Ecuyer-CMRG stream ... done") 520s *** randomSeed(): L'Ecuyer-CMRG stream ... done 520s > 520s > 520s > ## Cleanup 520s > message("*** randomSeed() - cleanup ...") 520s *** randomSeed() - cleanup ... 520s > genv <- globalenv() 520s > RNGkind("Mersenne-Twister") 520s > if (exists(".Random.seed", envir=genv, inherits=FALSE)) 520s + rm(list=".Random.seed", envir=genv, inherits=FALSE) 520s > rm(list=ovars, envir=globalenv()) 520s > message("*** randomSeed() - cleanup ... done") 520s *** randomSeed() - cleanup ... done 520s > 520s > proc.time() 520s user system elapsed 520s 2.064 0.418 2.436 520s + [ 0Test randomSeed passed 520s 0 520s Begin test segmentByCBS,calls 520s != 0 ] 520s + echo Test randomSeed passed 520s + echo 0 520s + echo Begin test segmentByCBS,calls 520s + exitcode=0 520s + R CMD BATCH segmentByCBS,calls.R 521s + cat segmentByCBS,calls.Rout 521s 521s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 521s Copyright (C) 2024 The R Foundation for Statistical Computing 521s Platform: aarch64-unknown-linux-gnu (64-bit) 521s 521s R is free software and comes with ABSOLUTELY NO WARRANTY. 521s You are welcome to redistribute it under certain conditions. 521s Type 'license()' or 'licence()' for distribution details. 521s 521s R is a collaborative project with many contributors. 521s Type 'contributors()' for more information and 521s 'citation()' on how to cite R or R packages in publications. 521s 521s Type 'demo()' for some demos, 'help()' for on-line help, or 521s 'help.start()' for an HTML browser interface to help. 521s Type 'q()' to quit R. 521s 521s [Previously saved workspace restored] 521s 521s > # This test script calls a report generator which requires 521s > # the 'ggplot2' package, which in turn will require packages 521s > # 'colorspace', 'dichromat', 'munsell', 'reshape2' and 'scales'. 521s > 521s > # Only run this test in full testing mode 521s > if (Sys.getenv("_R_CHECK_FULL_") != "") { 521s + library("PSCBS") 521s + stext <- R.utils::stext 521s + 521s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 521s + # Load SNP microarray data 521s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 521s + data <- PSCBS::exampleData("paired.chr01") 521s + str(data) 521s + 521s + data <- data.frame(chromosome=data$chromosome, x=data$x, y=data$CT) 521s + 521s + 521s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 521s + # CBS segmentation 521s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 521s + # Drop single-locus outliers 521s + dataS <- dropSegmentationOutliers(data) 521s + 521s + # Speed up example by segmenting fewer loci 521s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 521s + 521s + str(dataS) 521s + 521s + gaps <- findLargeGaps(dataS, minLength=2e6) 521s + knownSegments <- gapsToSegments(gaps) 521s + 521s + # CBS segmentation 521s + fit <- segmentByCBS(dataS, knownSegments=knownSegments, 521s + seed=0xBEEF, verbose=-10) 521s + signalType(fit) <- "ratio" 521s + plotTracks(fit) 521s + 521s + 521s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 521s + # Call using the UCSF MAD caller (not recommended) 521s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 521s + fitC <- callGainsAndLosses(fit) 521s + plotTracks(fitC) 521s + pars <- fitC$params$callGainsAndLosses 521s + stext(side=3, pos=1/2, line=-1, substitute(sigma==x, list(x=sprintf("%.2f", pars$sigmaMAD)))) 521s + mu <- pars$muR 521s + tau <- unlist(pars[c("tauLoss", "tauGain")], use.names=FALSE) 521s + abline(h=mu, lty=2, lwd=2) 521s + abline(h=tau, lwd=2) 521s + mtext(side=4, at=tau[1], expression(Delta[LOSS]), adj=-0.2, cex=0.7, las=2, xpd=TRUE) 521s + mtext(side=4, at=tau[2], expression(Delta[GAIN]), adj=-0.2, cex=0.7, las=2, xpd=TRUE) 521s + title(main="CN caller: \"ucsf-mad\"") 521s + 521s + 521s + # Caller to be implemented 521s + deltaCN <- estimateDeltaCN(fit) 521s + tau <- mu + 1/2*c(-1,+1)*deltaCN 521s + abline(h=tau, lty=2, lwd=1, col="red") 521s + 521s + 521s + 521s + } # if (Sys.getenv("_R_CHECK_FULL_")) 521s > 521s > proc.time() 521s user system elapsed 521s 0.660 0.269 0.769 521s Test segmentByCBS,calls passed 521s 0 521s Begin test segmentByCBS,futures 521s + [ 0 != 0 ] 521s + echo Test segmentByCBS,calls passed 521s + echo 0 521s + echo Begin test segmentByCBS,futures 521s + exitcode=0 521s + R CMD BATCH segmentByCBS,futures.R 534s + cat segmentByCBS,futures.Rout 534s 534s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 534s Copyright (C) 2024 The R Foundation for Statistical Computing 534s Platform: aarch64-unknown-linux-gnu (64-bit) 534s 534s R is free software and comes with ABSOLUTELY NO WARRANTY. 534s You are welcome to redistribute it under certain conditions. 534s Type 'license()' or 'licence()' for distribution details. 534s 534s R is a collaborative project with many contributors. 534s Type 'contributors()' for more information and 534s 'citation()' on how to cite R or R packages in publications. 534s 534s Type 'demo()' for some demos, 'help()' for on-line help, or 534s 'help.start()' for an HTML browser interface to help. 534s Type 'q()' to quit R. 534s 534s [Previously saved workspace restored] 534s 534s > library("PSCBS") 534s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 534s 534s Attaching package: 'PSCBS' 534s 534s The following objects are masked from 'package:base': 534s 534s append, load 534s 534s > 534s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 534s > # Simulating copy-number data 534s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 534s > set.seed(0xBEEF) 534s > 534s > # Number of loci 534s > J <- 1000 534s > 534s > mu <- double(J) 534s > mu[200:300] <- mu[200:300] + 1 534s > mu[350:400] <- NA # centromere 534s > mu[650:800] <- mu[650:800] - 1 534s > eps <- rnorm(J, sd=1/2) 534s > y <- mu + eps 534s > x <- sort(runif(length(y), max=length(y))) * 1e5 534s > w <- runif(J) 534s > w[650:800] <- 0.001 534s > 534s > ## Create multiple chromosomes 534s > data <- knownSegments <- list() 534s > for (cc in 1:3) { 534s + data[[cc]] <- data.frame(chromosome=cc, y=y, x=x) 534s + knownSegments[[cc]] <- data.frame( 534s + chromosome=c( cc, cc, cc), 534s + start =x[c( 1, 350, 401)], 534s + end =x[c(349, 400, J)] 534s + ) 534s + } 534s > data <- Reduce(rbind, data) 534s > str(data) 534s 'data.frame': 3000 obs. of 3 variables: 534s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 534s $ y : num 0.295 0.115 -0.194 -0.392 -0.518 ... 534s $ x : num 55168 593204 605649 630624 746896 ... 534s > knownSegments <- Reduce(rbind, knownSegments) 534s > str(knownSegments) 534s 'data.frame': 9 obs. of 3 variables: 534s $ chromosome: int 1 1 1 2 2 2 3 3 3 534s $ start : num 55168 34194740 41080533 55168 34194740 ... 534s $ end : num 34142178 41044125 99910827 34142178 41044125 ... 534s > 534s > message("*** segmentByCBS() via futures ...") 534s *** segmentByCBS() via futures ... 534s > 534s > 534s > message("*** segmentByCBS() via futures with 'future' attached ...") 534s *** segmentByCBS() via futures with 'future' attached ... 534s > library("future") 534s > oplan <- plan() 534s > 534s > strategies <- c("sequential", "multisession") 534s > 534s > ## Test 'future.batchtools' futures? 534s > pkg <- "future.batchtools" 534s > if (require(pkg, character.only=TRUE)) { 534s + strategies <- c(strategies, "batchtools_local") 534s + } 534s Loading required package: future.batchtools 534s Warning message: 534s In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : 534s there is no package called 'future.batchtools' 534s > 534s > message("Future strategies to test: ", paste(sQuote(strategies), collapse=", ")) 534s Future strategies to test: 'sequential', 'multisession' 534s > 534s > fits <- list() 534s > for (strategy in strategies) { 534s + message(sprintf("- segmentByCBS() using '%s' futures ...", strategy)) 534s + plan(strategy) 534s + fit <- segmentByCBS(data, seed=0xBEEF, verbose=TRUE) 534s + fits[[strategy]] <- fit 534s + stopifnot(all.equal(fit, fits[[1]])) 534s + } 534s - segmentByCBS() using 'sequential' futures ... 534s Segmenting by CBS... 534s Segmenting multiple chromosomes... 534s Number of chromosomes: 3 534s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 534s Produced 3 seeds from this stream for future usage 534s Chromosome #1 ('Chr01') of 3... 534s Segmenting by CBS... 534s Chromosome: 1 534s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 534s Segmenting by CBS...done 534s Chromosome #1 ('Chr01') of 3...done 534s Chromosome #2 ('Chr02') of 3... 534s Segmenting by CBS... 534s Chromosome: 2 534s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 534s Segmenting by CBS...done 534s Chromosome #2 ('Chr02') of 3...done 534s Chromosome #3 ('Chr03') of 3... 534s Segmenting by CBS... 534s Chromosome: 3 534s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 534s Segmenting by CBS...done 534s Chromosome #3 ('Chr03') of 3...done 534s Segmenting multiple chromosomes...done 534s Segmenting by CBS...done 534s list() 534s - segmentByCBS() using 'multisession' futures ... 534s Segmenting by CBS... 534s Segmenting multiple chromosomes... 534s Number of chromosomes: 3 534s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 534s Produced 3 seeds from this stream for future usage 534s Chromosome #1 ('Chr01') of 3... 534s Segmenting by CBS... 534s Chromosome: 1 534s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 534s Segmenting by CBS...done 534s Chromosome #1 ('Chr01') of 3...done 534s Chromosome #2 ('Chr02') of 3... 534s Segmenting by CBS... 534s Chromosome: 2 534s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 534s Segmenting by CBS...done 534s Chromosome #2 ('Chr02') of 3...done 534s Chromosome #3 ('Chr03') of 3... 534s Segmenting by CBS... 534s Chromosome: 3 534s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 534s Segmenting by CBS...done 534s Chromosome #3 ('Chr03') of 3...done 534s Segmenting multiple chromosomes...done 534s Segmenting by CBS...done 534s list() 534s > 534s > 534s > message("*** segmentByCBS() via futures with known segments ...") 534s *** segmentByCBS() via futures with known segments ... 534s > fits <- list() 534s > dataT <- subset(data, chromosome == 1) 534s > for (strategy in strategies) { 534s + message(sprintf("- segmentByCBS() w/ known segments using '%s' futures ...", strategy)) 534s + plan(strategy) 534s + fit <- segmentByCBS(dataT, knownSegments=knownSegments, seed=0xBEEF, verbose=TRUE) 534s + fits[[strategy]] <- fit 534s + stopifnot(all.equal(fit, fits[[1]])) 534s + } 534s - segmentByCBS() w/ known segments using 'sequential' futures ... 534s Segmenting by CBS... 534s Chromosome: 1 534s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 534s Produced 3 seeds from this stream for future usage 534s Segmenting by CBS...done 534s list() 534s - segmentByCBS() w/ known segments using 'multisession' futures ... 534s Segmenting by CBS... 534s Chromosome: 1 534s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 534s Produced 3 seeds from this stream for future usage 534s Segmenting by CBS...done 534s list() 534s > 534s > message("*** segmentByCBS() via futures ... DONE") 534s *** segmentByCBS() via futures ... DONE 534s > 534s > 534s > ## Cleanup 534s > plan(oplan) 534s > rm(list=c("fits", "dataT", "data", "fit")) 534s > 534s > 534s > proc.time() 534s user system elapsed 534s 11.596 0.799 12.388 534s Test segmentByCBS,futures passed 534s 0 534s Begin test segmentByCBS,median 534s + [ 0 != 0 ] 534s + echo Test segmentByCBS,futures passed 534s + echo 0 534s + echo Begin test segmentByCBS,median 534s + exitcode=0 534s + R CMD BATCH segmentByCBS,median.R 543s + cat segmentByCBS,median.Rout 543s 543s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 543s Copyright (C) 2024 The R Foundation for Statistical Computing 543s Platform: aarch64-unknown-linux-gnu (64-bit) 543s 543s R is free software and comes with ABSOLUTELY NO WARRANTY. 543s You are welcome to redistribute it under certain conditions. 543s Type 'license()' or 'licence()' for distribution details. 543s 543s R is a collaborative project with many contributors. 543s Type 'contributors()' for more information and 543s 'citation()' on how to cite R or R packages in publications. 543s 543s Type 'demo()' for some demos, 'help()' for on-line help, or 543s 'help.start()' for an HTML browser interface to help. 543s Type 'q()' to quit R. 543s 543s [Previously saved workspace restored] 543s 543s > library("PSCBS") 543s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 543s 543s Attaching package: 'PSCBS' 543s 543s The following objects are masked from 'package:base': 543s 543s append, load 543s 543s > 543s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 543s > # Simulating copy-number data 543s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 543s > set.seed(0xBEEF) 543s > 543s > # Number of loci 543s > J <- 1000 543s > 543s > x <- sort(runif(J, max=J)) * 1e5 543s > 543s > mu <- double(J) 543s > mu[200:300] <- mu[200:300] + 1 543s > mu[350:400] <- NA # centromere 543s > mu[650:800] <- mu[650:800] - 1 543s > eps <- rnorm(J, sd=1/2) 543s > y <- mu + eps 543s > 543s > outliers <- seq(from=1L, to=J, length.out=0.2*J) 543s > y[outliers] <- y[outliers] + 1.5 543s > 543s > w <- rep(1.0, times=J) 543s > w[outliers] <- 0.01 543s > 543s > data <- data.frame(chromosome=1L, x=x, y=y) 543s > dataW <- cbind(data, w=w) 543s > 543s > 543s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 543s > # Single-chromosome segmentation 543s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 543s > par(mar=c(2,3,0.2,1)+0.1) 543s > # Segment without weights 543s > fit <- segmentByCBS(data) 543s > sampleName(fit) <- "CBS_Example" 543s > print(fit) 543s sampleName chromosome start end nbrOfLoci mean 543s 1 CBS_Example 1 6.066868e+02 19076007 199 0.2622 543s 2 CBS_Example 1 1.907601e+07 29630949 99 1.4289 543s 3 CBS_Example 1 2.963095e+07 63224332 299 0.2854 543s 4 CBS_Example 1 6.322433e+07 78801707 153 -0.7408 543s 5 CBS_Example 1 7.880171e+07 99917418 199 0.3541 543s > plotTracks(fit) 543s Warning message: 543s In plotTracks.CBS(fit) : 543s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit) is unknown ('NA'). Use signalType(fit) <- 'ratio' to avoid this warning. 543s > ## Highlight outliers (they pull up the mean levels) 543s > points(x[outliers]/1e6, y[outliers], col="purple") 543s > 543s > # Segment without weights but with median 543s > fitM <- segmentByCBS(data, avg="median") 543s > sampleName(fitM) <- "CBS_Example (median)" 543s > print(fitM) 543s sampleName chromosome start end nbrOfLoci mean 543s 1 CBS_Example (median) 1 6.066868e+02 19076007 199 0.1005418 543s 2 CBS_Example (median) 1 1.907601e+07 29630949 99 1.2720955 543s 3 CBS_Example (median) 1 2.963095e+07 63224332 299 0.1337148 543s 4 CBS_Example (median) 1 6.322433e+07 78801707 153 -0.8655254 543s 5 CBS_Example (median) 1 7.880171e+07 99917418 199 0.1718179 543s > drawLevels(fitM, col="magenta", lty=3) 543s NULL 543s > 543s > # Segment with weights 543s > fitW <- segmentByCBS(dataW, avg="median") 543s > sampleName(fitW) <- "CBS_Example (weighted)" 543s > print(fitW) 543s sampleName chromosome start end nbrOfLoci mean 543s 1 CBS_Example (weighted) 1 6.066868e+02 19076007 199 -0.08745973 543s 2 CBS_Example (weighted) 1 1.907601e+07 30126128 101 1.12968951 543s 3 CBS_Example (weighted) 1 3.012613e+07 63224332 297 -0.06074638 543s 4 CBS_Example (weighted) 1 6.322433e+07 78801707 153 -1.06373835 543s 5 CBS_Example (weighted) 1 7.880171e+07 99917418 199 0.04204744 543s > drawLevels(fitW, col="red") 543s NULL 543s > 543s > # Segment with weights and median 543s > fitWM <- segmentByCBS(dataW, avg="median") 543s > sampleName(fitWM) <- "CBS_Example (weighted median)" 543s > print(fitWM) 543s sampleName chromosome start end nbrOfLoci 543s 1 CBS_Example (weighted median) 1 6.066868e+02 19076007 199 543s 2 CBS_Example (weighted median) 1 1.907601e+07 30126128 101 543s 3 CBS_Example (weighted median) 1 3.012613e+07 63224332 297 543s 4 CBS_Example (weighted median) 1 6.322433e+07 78801707 153 543s 5 CBS_Example (weighted median) 1 7.880171e+07 99917418 199 543s mean 543s 1 -0.08745973 543s 2 1.12968951 543s 3 -0.06074638 543s 4 -1.06373835 543s 5 0.04204744 543s > drawLevels(fitWM, col="orange", lty=3) 543s NULL 543s > 543s > legend("topright", bg="white", legend=c("outliers", "non-weighted CBS (mean)", "non-weighted CBS (median)", "weighted CBS (mean)", "weighted CBS (median)"), col=c("purple", "purple", "magenta", "red", "orange"), lwd=c(NA,3,3,3,3), lty=c(NA,1,3,1,3), pch=c(1,NA,NA,NA,NA)) 543s > 543s > ## Assert that weighted segment means are less biased 543s > dmean <- getSegments(fit)$mean - getSegments(fitW)$mean 543s > cat("Segment mean differences:\n") 543s Segment mean differences: 543s > print(dmean) 543s [1] 0.3496597 0.2992105 0.3461464 0.3229384 0.3120526 543s > stopifnot(all(dmean > 0, na.rm=TRUE)) 543s > 543s > dmean <- getSegments(fitM)$mean - getSegments(fitWM)$mean 543s > cat("Segment median differences:\n") 543s Segment median differences: 543s > print(dmean) 543s [1] 0.1880015 0.1424060 0.1944611 0.1982130 0.1297704 543s > stopifnot(all(dmean > 0, na.rm=TRUE)) 543s > 543s > 543s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 543s > # Multi-chromosome segmentation 543s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 543s > data2 <- data 543s > data2$chromosome <- 2L 543s > data <- rbind(data, data2) 543s > dataW <- cbind(data, w=w) 543s > 543s > par(mar=c(2,3,0.2,1)+0.1) 543s > # Segment without weights 543s > fit <- segmentByCBS(data) 543s > sampleName(fit) <- "CBS_Example" 543s > print(fit) 543s sampleName chromosome start end nbrOfLoci mean 543s 1 CBS_Example 1 6.066868e+02 19076007 199 0.2622 543s 2 CBS_Example 1 1.907601e+07 29630949 99 1.4289 543s 3 CBS_Example 1 2.963095e+07 63224332 299 0.2854 543s 4 CBS_Example 1 6.322433e+07 78801707 153 -0.7408 543s 5 CBS_Example 1 7.880171e+07 99917418 199 0.3541 543s 6 NA NA NA NA NA 543s 7 CBS_Example 2 6.066868e+02 19076007 199 0.2622 543s 8 CBS_Example 2 1.907601e+07 29630949 99 1.4289 543s 9 CBS_Example 2 2.963095e+07 63224332 299 0.2854 543s 10 CBS_Example 2 6.322433e+07 78801707 153 -0.7408 543s 11 CBS_Example 2 7.880171e+07 99917418 199 0.3541 543s > plotTracks(fit, Clim=c(-3,3)) 543s > 543s > # Segment without weights but with median 543s > fitM <- segmentByCBS(data, avg="median") 543s > sampleName(fitM) <- "CBS_Example (median)" 543s > print(fitM) 543s sampleName chromosome start end nbrOfLoci mean 543s 1 CBS_Example (median) 1 6.066868e+02 19076007 199 0.1005418 543s 2 CBS_Example (median) 1 1.907601e+07 29630949 99 1.2720955 543s 3 CBS_Example (median) 1 2.963095e+07 63224332 299 0.1337148 543s 4 CBS_Example (median) 1 6.322433e+07 78801707 153 -0.8655254 543s 5 CBS_Example (median) 1 7.880171e+07 99917418 199 0.1718179 543s 6 NA NA NA NA NA 543s 7 CBS_Example (median) 2 6.066868e+02 19076007 199 0.1005418 543s 8 CBS_Example (median) 2 1.907601e+07 29630949 99 1.2720955 543s 9 CBS_Example (median) 2 2.963095e+07 63224332 299 0.1337148 543s 10 CBS_Example (median) 2 6.322433e+07 78801707 153 -0.8655254 543s 11 CBS_Example (median) 2 7.880171e+07 99917418 199 0.1718179 543s > drawLevels(fitM, col="magenta", lty=3) 543s NULL 543s > 543s > # Segment with weights 543s > fitW <- segmentByCBS(dataW, avg="median") 543s > sampleName(fitW) <- "CBS_Example (weighted)" 543s > print(fitW) 543s sampleName chromosome start end nbrOfLoci 543s 1 CBS_Example (weighted) 1 6.066868e+02 19076007 199 543s 2 CBS_Example (weighted) 1 1.907601e+07 30126128 101 543s 3 CBS_Example (weighted) 1 3.012613e+07 63224332 297 543s 4 CBS_Example (weighted) 1 6.322433e+07 78801707 153 543s 5 CBS_Example (weighted) 1 7.880171e+07 99917418 199 543s 6 NA NA NA NA 543s 7 CBS_Example (weighted) 2 6.066868e+02 19076007 199 543s 8 CBS_Example (weighted) 2 1.907601e+07 30126128 101 543s 9 CBS_Example (weighted) 2 3.012613e+07 63224332 297 543s 10 CBS_Example (weighted) 2 6.322433e+07 78801707 153 543s 11 CBS_Example (weighted) 2 7.880171e+07 99917418 199 543s mean 543s 1 -0.08745973 543s 2 1.12968951 543s 3 -0.06074638 543s 4 -1.06373835 543s 5 0.04204744 543s 6 NA 543s 7 -0.08745973 543s 8 1.12968951 543s 9 -0.06074638 543s 10 -1.06373835 543s 11 0.04204744 543s > drawLevels(fitW, col="red") 543s NULL 543s > 543s > # Segment with weights and median 543s > fitWM <- segmentByCBS(dataW, avg="median") 543s > sampleName(fitWM) <- "CBS_Example (weighted median)" 543s > print(fitWM) 543s sampleName chromosome start end nbrOfLoci 543s 1 CBS_Example (weighted median) 1 6.066868e+02 19076007 199 543s 2 CBS_Example (weighted median) 1 1.907601e+07 30126128 101 543s 3 CBS_Example (weighted median) 1 3.012613e+07 63224332 297 543s 4 CBS_Example (weighted median) 1 6.322433e+07 78801707 153 543s 5 CBS_Example (weighted median) 1 7.880171e+07 99917418 199 543s 6 NA NA NA NA 543s 7 CBS_Example (weighted median) 2 6.066868e+02 19076007 199 543s 8 CBS_Example (weighted median) 2 1.907601e+07 30126128 101 543s 9 CBS_Example (weighted median) 2 3.012613e+07 63224332 297 543s 10 CBS_Example (weighted median) 2 6.322433e+07 78801707 153 543s 11 CBS_Example (weighted median) 2 7.880171e+07 99917418 199 543s mean 543s 1 -0.08745973 543s 2 1.12968951 543s 3 -0.06074638 543s 4 -1.06373835 543s 5 0.04204744 543s 6 NA 543s 7 -0.08745973 543s 8 1.12968951 543s 9 -0.06074638 543s 10 -1.06373835 543s 11 0.04204744 543s > drawLevels(fitWM, col="orange", lty=3) 543s NULL 543s > 543s > legend("topright", bg="white", legend=c("outliers", "non-weighted CBS (mean)", "non-weighted CBS (median)", "weighted CBS (mean)", "weighted CBS (median)"), col=c("purple", "purple", "magenta", "red", "orange"), lwd=c(NA,3,3,3,3), lty=c(NA,1,3,1,3), pch=c(1,NA,NA,NA,NA)) 543s > 543s > ## Assert that weighted segment means are less biased 543s > dmean <- getSegments(fit)$mean - getSegments(fitW)$mean 543s > cat("Segment mean differences:\n") 543s Segment mean differences: 543s > print(dmean) 543s [1] 0.3496597 0.2992105 0.3461464 0.3229384 0.3120526 NA 0.3496597 543s [8] 0.2992105 0.3461464 0.3229384 0.3120526 543s > stopifnot(all(dmean > 0, na.rm=TRUE)) 543s > 543s > dmean <- getSegments(fitM)$mean - getSegments(fitWM)$mean 543s > cat("Segment median differences:\n") 543s Segment median differences: 543s > print(dmean) 543s [1] 0.1880015 0.1424060 0.1944611 0.1982130 0.1297704 NA 0.1880015 543s [8] 0.1424060 0.1944611 0.1982130 0.1297704 543s > stopifnot(all(dmean > 0, na.rm=TRUE)) 543s > 543s > proc.time() 543s user system elapsed 543s 8.032 0.493 8.492 543s Test segmentByCBS,median passed 543s 0 543s Begin test segmentByCBS,prune 543s + [ 0 != 0 ] 543s + echo Test segmentByCBS,median passed 543s + echo 0 543s + echo Begin test segmentByCBS,prune 543s + exitcode=0 543s + R CMD BATCH segmentByCBS,prune.R 549s + cat segmentByCBS,prune.Rout 549s + [ 0 != 0 ] 549s + echo Test segmentByCBS,prune passed 549s + echo 0 549s + echo Begin test segmentByCBS,report 549s + exitcode=0 549s + R CMD BATCH segmentByCBS,report.R 549s 549s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 549s Copyright (C) 2024 The R Foundation for Statistical Computing 549s Platform: aarch64-unknown-linux-gnu (64-bit) 549s 549s R is free software and comes with ABSOLUTELY NO WARRANTY. 549s You are welcome to redistribute it under certain conditions. 549s Type 'license()' or 'licence()' for distribution details. 549s 549s R is a collaborative project with many contributors. 549s Type 'contributors()' for more information and 549s 'citation()' on how to cite R or R packages in publications. 549s 549s Type 'demo()' for some demos, 'help()' for on-line help, or 549s 'help.start()' for an HTML browser interface to help. 549s Type 'q()' to quit R. 549s 549s [Previously saved workspace restored] 549s 549s > library("PSCBS") 549s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 549s 549s Attaching package: 'PSCBS' 549s 549s The following objects are masked from 'package:base': 549s 549s append, load 549s 549s > 549s > ## Compare segments 549s > assertMatchingSegments <- function(fitM, fit) { 549s + chrs <- getChromosomes(fitM) 549s + segsM <- lapply(chrs, FUN=function(chr) { 549s + getSegments(extractChromosome(fitM, chr)) 549s + }) 549s + segs <- lapply(fit[chrs], FUN=getSegments) 549s + stopifnot(all.equal(segsM, segs, check.attributes=FALSE)) 549s + } 549s > 549s > ## Simulate data 549s > set.seed(0xBEEF) 549s > J <- 1000 549s > mu <- double(J) 549s > mu[200:300] <- mu[200:300] + 1 549s > mu[350:400] <- NA 549s > mu[650:800] <- mu[650:800] - 1 549s > eps <- rnorm(J, sd=1/2) 549s > y <- mu + eps 549s > x <- sort(runif(length(y), max=length(y))) * 1e5 549s > 549s > data <- list() 549s > for (chr in 1:2) { 549s + data[[chr]] <- data.frame(chromosome=chr, x=x, y=y) 549s + } 549s > data$M <- Reduce(rbind, data) 549s > 549s > ## Segment 549s > message("*** segmentByCBS()") 549s *** segmentByCBS() 549s > fit <- lapply(data, FUN=segmentByCBS) 549s > print(fit) 549s [[1]] 549s sampleName chromosome start end nbrOfLoci mean 549s 1 1 65285.65 19648927 200 0.0109 549s 2 1 19648927.46 28239656 95 0.9529 549s 3 1 28239655.99 65697742 302 -0.0126 549s 4 1 65697742.20 79729368 153 -0.9534 549s 5 1 79729368.34 99819310 199 -0.0497 549s 549s [[2]] 549s sampleName chromosome start end nbrOfLoci mean 549s 1 2 65285.65 19648927 200 0.0109 549s 2 2 19648927.46 28239656 95 0.9529 549s 3 2 28239655.99 65697742 302 -0.0126 549s 4 2 65697742.20 79729368 153 -0.9534 549s 5 2 79729368.34 99819310 199 -0.0497 549s 549s $M 549s sampleName chromosome start end nbrOfLoci mean 549s 1 1 65285.65 19648927 200 0.0109 549s 2 1 19648927.46 28239656 95 0.9529 549s 3 1 28239655.99 65697742 302 -0.0126 549s 4 1 65697742.20 79729368 153 -0.9534 549s 5 1 79729368.34 99819310 199 -0.0497 549s 6 NA NA NA NA NA 549s 7 2 65285.65 19648927 200 0.0109 549s 8 2 19648927.46 28239656 95 0.9529 549s 9 2 28239655.99 65697742 302 -0.0126 549s 10 2 65697742.20 79729368 153 -0.9534 549s 11 2 79729368.34 99819310 199 -0.0497 549s 549s > assertMatchingSegments(fit$M, fit) 549s > 549s > ## Join segments 549s > message("*** joinSegments()") 549s *** joinSegments() 549s > fitj <- lapply(fit, FUN=joinSegments) 549s > print(fitj) 549s [[1]] 549s sampleName chromosome start end nbrOfLoci mean 549s 1 1 65285.65 19648927 200 0.0109 549s 2 1 19648927.46 28239656 95 0.9529 549s 3 1 28239655.99 65697742 302 -0.0126 549s 4 1 65697742.20 79729368 153 -0.9534 549s 5 1 79729368.34 99819310 199 -0.0497 549s 549s [[2]] 549s sampleName chromosome start end nbrOfLoci mean 549s 1 2 65285.65 19648927 200 0.0109 549s 2 2 19648927.46 28239656 95 0.9529 549s 3 2 28239655.99 65697742 302 -0.0126 549s 4 2 65697742.20 79729368 153 -0.9534 549s 5 2 79729368.34 99819310 199 -0.0497 549s 549s $M 549s sampleName chromosome start end nbrOfLoci mean 549s 1 1 65285.65 19648927 200 0.0109 549s 2 1 19648927.46 28239656 95 0.9529 549s 3 1 28239655.99 65697742 302 -0.0126 549s 4 1 65697742.20 79729368 153 -0.9534 549s 5 1 79729368.34 99819310 199 -0.0497 549s 6 NA NA NA NA NA 549s 7 2 65285.65 19648927 200 0.0109 549s 8 2 19648927.46 28239656 95 0.9529 549s 9 2 28239655.99 65697742 302 -0.0126 549s 10 2 65697742.20 79729368 153 -0.9534 549s 11 2 79729368.34 99819310 199 -0.0497 549s 549s > assertMatchingSegments(fitj$M, fitj) 549s > 549s > ## Reset segments 549s > message("*** resetSegments()") 549s *** resetSegments() 549s > fitj <- lapply(fit, FUN=resetSegments) 549s > print(fitj) 549s [[1]] 549s sampleName chromosome start end nbrOfLoci mean 549s 1 1 65285.65 19648927 200 0.0109 549s 2 1 19648927.46 28239656 95 0.9529 549s 3 1 28239655.99 65697742 302 -0.0126 549s 4 1 65697742.20 79729368 153 -0.9534 549s 5 1 79729368.34 99819310 199 -0.0497 549s 549s [[2]] 549s sampleName chromosome start end nbrOfLoci mean 549s 1 2 65285.65 19648927 200 0.0109 549s 2 2 19648927.46 28239656 95 0.9529 549s 3 2 28239655.99 65697742 302 -0.0126 549s 4 2 65697742.20 79729368 153 -0.9534 549s 5 2 79729368.34 99819310 199 -0.0497 549s 549s $M 549s sampleName chromosome start end nbrOfLoci mean 549s 1 1 65285.65 19648927 200 0.0109 549s 2 1 19648927.46 28239656 95 0.9529 549s 3 1 28239655.99 65697742 302 -0.0126 549s 4 1 65697742.20 79729368 153 -0.9534 549s 5 1 79729368.34 99819310 199 -0.0497 549s 6 NA NA NA NA NA 549s 7 2 65285.65 19648927 200 0.0109 549s 8 2 19648927.46 28239656 95 0.9529 549s 9 2 28239655.99 65697742 302 -0.0126 549s 10 2 65697742.20 79729368 153 -0.9534 549s 11 2 79729368.34 99819310 199 -0.0497 549s 549s > assertMatchingSegments(fitj$M, fitj) 549s > 549s > ## Prune by SD undo 549s > message("*** pruneBySdUndo()") 549s *** pruneBySdUndo() 549s > fitp <- lapply(fit, FUN=pruneBySdUndo) 549s > print(fitp) 549s [[1]] 549s sampleName chromosome start end nbrOfLoci mean 549s 1 1 65285.65 99819310 949 -0.07045097 549s 549s [[2]] 549s sampleName chromosome start end nbrOfLoci mean 549s 1 2 65285.65 99819310 949 -0.07045097 549s 549s $M 549s sampleName chromosome start end nbrOfLoci mean 549s 1 1 65285.65 99819310 949 -0.07045097 549s 2 NA NA NA NA NA 549s 3 2 65285.65 99819310 949 -0.07045097 549s 549s > assertMatchingSegments(fitp$M, fitp) 549s > 549s > ## Prune by hierarchical clustering 549s > message("*** pruneByHClust()") 549s *** pruneByHClust() 549s > fitp <- lapply(fit, FUN=pruneByHClust, k=1L) 549s > print(fitp) 549s [[1]] 549s sampleName chromosome start end nbrOfLoci mean 549s 1 1 65285.65 99819310 949 -0.07045097 549s 549s [[2]] 549s sampleName chromosome start end nbrOfLoci mean 549s 1 2 65285.65 99819310 949 -0.07045097 549s 549s $M 549s sampleName chromosome start end nbrOfLoci mean 549s 1 1 65285.65 99819310 949 -0.07045097 549s 6 NA NA NA NA NA 549s 7 2 65285.65 99819310 949 -0.07045097 549s 549s > assertMatchingSegments(fitp$M, fitp) 549s > 549s > proc.time() 549s user system elapsed 549s 4.848 0.430 5.240 549s Test segmentByCBS,prune passed 549s 0 549s Begin test segmentByCBS,report 551s + cat segmentByCBS,report.Rout 551s 551s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 551s Copyright (C) 2024 The R Foundation for Statistical Computing 551s Platform: aarch64-unknown-linux-gnu (64-bit) 551s 551s R is free software and comes with ABSOLUTELY NO WARRANTY. 551s You are welcome to redistribute it under certain conditions. 551s Type 'license()' or 'licence()' for distribution details. 551s 551s R is a collaborative project with many contributors. 551s Type 'contributors()' for more information and 551s 'citation()' on how to cite R or R packages in publications. 551s 551s Type 'demo()' for some demos, 'help()' for on-line help, or 551s 'help.start()' for an HTML browser interface to help. 551s Type 'q()' to quit R. 551s 551s [Previously saved workspace restored] 551s 551s > # This test script calls a report generator which requires 551s > # the 'ggplot2' package, which in turn will require packages 551s > # 'colorspace', 'dichromat', 'munsell', 'reshape2' and 'scales'. 551s > 551s > # Only run this test in full testing mode 551s > if (Sys.getenv("_R_CHECK_FULL_") != "") { 551s + library("PSCBS") 551s + 551s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 551s + # Load SNP microarray data 551s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 551s + data <- PSCBS::exampleData("paired.chr01") 551s + str(data) 551s + 551s + data <- data.frame(chromosome=data$chromosome, x=data$x, y=data$CT) 551s + 551s + 551s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 551s + # CBS segmentation 551s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 551s + # Drop single-locus outliers 551s + dataS <- dropSegmentationOutliers(data) 551s + 551s + # Speed up example by segmenting fewer loci 551s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 551s + 551s + str(dataS) 551s + 551s + gaps <- findLargeGaps(dataS, minLength=2e6) 551s + knownSegments <- gapsToSegments(gaps) 551s + 551s + # CBS segmentation 551s + fit <- segmentByCBS(dataS, knownSegments=knownSegments, 551s + seed=0xBEEF, verbose=-10) 551s + signalType(fit) <- "ratio" 551s + 551s + # Fake a multi-chromosome segmentation 551s + fit1 <- fit 551s + fit2 <- renameChromosomes(fit, from=1, to=2) 551s + fit <- c(fit1, fit2) 551s + 551s + report(fit, sampleName="CBS", studyName="CBS-Ex", verbose=-10) 551s + 551s + } # if (Sys.getenv("_R_CHECK_FULL_")) 551s > 551s > proc.time() 551s user system elapsed 551s 1.093 0.294 1.260 551s + [ 0 !=Test segmentByCBS,report passed 551s 0 551s Begin test segmentByCBS,shiftTCN 551s 0 ] 551s + echo Test segmentByCBS,report passed 551s + echo 0 551s + echo Begin test segmentByCBS,shiftTCN 551s + exitcode=0 551s + R CMD BATCH segmentByCBS,shiftTCN.R 605s + cat segmentByCBS,shiftTCN.Rout 605s 605s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 605s Copyright (C) 2024 The R Foundation for Statistical Computing 605s Platform: aarch64-unknown-linux-gnu (64-bit) 605s 605s R is free software and comes with ABSOLUTELY NO WARRANTY. 605s You are welcome to redistribute it under certain conditions. 605s Type 'license()' or 'licence()' for distribution details. 605s 605s R is a collaborative project with many contributors. 605s Type 'contributors()' for more information and 605s 'citation()' on how to cite R or R packages in publications. 605s 605s Type 'demo()' for some demos, 'help()' for on-line help, or 605s 'help.start()' for an HTML browser interface to help. 605s Type 'q()' to quit R. 605s 605s [Previously saved workspace restored] 605s 605s > library("PSCBS") 605s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 605s 605s Attaching package: 'PSCBS' 605s 605s The following objects are masked from 'package:base': 605s 605s append, load 605s 605s > subplots <- R.utils::subplots 605s > 605s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 605s > # Simulating copy-number data 605s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 605s > set.seed(0xBEEF) 605s > 605s > # Number of loci 605s > J <- 1000 605s > 605s > mu <- double(J) 605s > eps <- rnorm(J, sd=1/2) 605s > y <- mu + eps 605s > x <- sort(runif(length(y), max=length(y))) 605s > 605s > idxs <- which(200 <= x & x < 300) 605s > y[idxs] <- y[idxs] + 1 605s > idxs <- which(350 <= x & x < 400) 605s > y[idxs] <- NA # centromere 605s > x[idxs] <- NA # centromere 605s > idxs <- which(650 <= x & x < 800) 605s > y[idxs] <- y[idxs] - 1 605s > x <- x*1e5 605s > 605s > keep <- is.finite(x) 605s > x <- x[keep] 605s > y <- y[keep] 605s > 605s > data <- list() 605s > for (chr in 1:2) { 605s + data[[chr]] <- data.frame(chromosome=chr, y=y, x=x) 605s + } 605s > data <- Reduce(rbind, data) 605s > 605s > 605s > subplots(7, ncol=1) 605s > par(mar=c(1.7,1,0.2,1)+0.1) 605s > 605s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 605s > # Segmentation 605s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 605s > fit <- segmentByCBS(data) 605s > print(fit) 605s sampleName chromosome start end nbrOfLoci mean 605s 1 1 65285.65 20169684 205 0.0124 605s 2 1 20169684.05 29980147 103 0.9477 605s 3 1 29980147.36 64779929 287 -0.0299 605s 4 1 64779929.38 80010171 163 -0.9676 605s 5 1 80010171.14 99819310 196 -0.0484 605s 6 NA NA NA NA NA 605s 7 2 65285.65 20169684 205 0.0124 605s 8 2 20169684.05 29980147 103 0.9477 605s 9 2 29980147.36 64779929 287 -0.0299 605s 10 2 64779929.38 80010171 163 -0.9676 605s 11 2 80010171.14 99819310 196 -0.0484 605s > 605s > Clim <- c(-3,3) + c(0,10) 605s > plotTracks(fit, Clim=Clim) 605s > 605s > 605s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 605s > # Shifting every other chromosome 605s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 605s > fitList <- list() 605s > chrs <- getChromosomes(fit) 605s > for (kk in seq_along(chrs)) { 605s + chr <- chrs[kk] 605s + fitKK <- extractChromosome(fit, chr) 605s + if (kk %% 2 == 0) { 605s + fitKK <- shiftTCN(fitKK, shift=+10) 605s + } 605s + fitList[[kk]] <- fitKK 605s + } # for (kk ...) 605s > fitT <- do.call(c, fitList) 605s > # Sanity check 605s > stopifnot(nbrOfSegments(fitT) == nbrOfSegments(fit)) 605s > 605s > plotTracks(fitT, Clim=Clim) 605s > 605s > 605s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 605s > # Shifting every other known segment 605s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 605s > gaps <- findLargeGaps(data, minLength=40e5) 605s > knownSegments <- gapsToSegments(gaps, dropGaps=TRUE) 605s > fit <- segmentByCBS(data, knownSegments=knownSegments) 605s > 605s > subplots(2, ncol=1) 605s > plotTracks(fit, Clim=Clim) 605s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 605s > 605s > fitList <- list() 605s > for (kk in seq_len(nrow(knownSegments))) { 605s + seg <- knownSegments[kk,] 605s + start <- seg$start 605s + end <- seg$end 605s + fitKK <- extractChromosome(fit, seg$chromosome) 605s + segsKK <- getSegments(fitKK) 605s + idxStart <- min(which(segsKK$start >= start)) 605s + idxEnd <- max(which(segsKK$end <= end)) 605s + idxs <- idxStart:idxEnd 605s + fitKK <- extractSegments(fitKK, idxs) 605s + if (kk %% 2 == 0) { 605s + fitKK <- shiftTCN(fitKK, shift=+10) 605s + } 605s + fitList[[kk]] <- fitKK 605s + } # for (kk ...) 605s > fitT <- do.call(c, fitList) 605s > # Sanity check 605s > stopifnot(nbrOfSegments(fitT) == nbrOfSegments(fit)) 605s > 605s > plotTracks(fitT, Clim=Clim) 605s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 605s > 605s > 605s > segList <- seqOfSegmentsByDP(fit) 605s > K <- length(segList) 605s > subplots(K, ncol=2, byrow=FALSE) 605s > par(mar=c(2,1,1,1)) 605s > for (kk in 1:K) { 605s + knownSegments <- segList[[kk]] 605s + fitKK <- resegment(fit, knownSegments=knownSegments, undo=+Inf) 605s + plotTracks(fitKK, Clim=c(-3,3)) 605s + } # for (kk ...) 605s > 605s > proc.time() 605s user system elapsed 605s 51.660 0.950 52.668 605s + [ 0Test segmentByCBS,shiftTCN passed 605s 0 605s Begin test segmentByCBS,weights 605s != 0 ] 605s + echo Test segmentByCBS,shiftTCN passed 605s + echo 0 605s + echo Begin test segmentByCBS,weights 605s + exitcode=0 605s + R CMD BATCH segmentByCBS,weights.R 622s + cat segmentByCBS,weights.Rout 622s 622s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 622s Copyright (C) 2024 The R Foundation for Statistical Computing 622s Platform: aarch64-unknown-linux-gnu (64-bit) 622s 622s R is free software and comes with ABSOLUTELY NO WARRANTY. 622s You are welcome to redistribute it under certain conditions. 622s Type 'license()' or 'licence()' for distribution details. 622s 622s R is a collaborative project with many contributors. 622s Type 'contributors()' for more information and 622s 'citation()' on how to cite R or R packages in publications. 622s 622s Type 'demo()' for some demos, 'help()' for on-line help, or 622s 'help.start()' for an HTML browser interface to help. 622s Type 'q()' to quit R. 622s 622s [Previously saved workspace restored] 622s 622s > library("PSCBS") 622s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 622s 622s Attaching package: 'PSCBS' 622s 622s The following objects are masked from 'package:base': 622s 622s append, load 622s 622s > 622s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 622s > # Simulating copy-number data 622s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 622s > set.seed(0xBEEF) 622s > 622s > # Number of loci 622s > J <- 1000 622s > 622s > x <- sort(runif(J, max=J)) * 1e5 622s > 622s > mu <- double(J) 622s > mu[200:300] <- mu[200:300] + 1 622s > mu[350:400] <- NA # centromere 622s > mu[650:800] <- mu[650:800] - 1 622s > eps <- rnorm(J, sd=1/2) 622s > y <- mu + eps 622s > 622s > outliers <- seq(from=1L, to=J, length.out=0.2*J) 622s > y[outliers] <- y[outliers] + 1.5 622s > 622s > w <- rep(1.0, times=J) 622s > w[outliers] <- 0.01 622s > 622s > data <- data.frame(chromosome=1L, x=x, y=y) 622s > dataW <- cbind(data, w=w) 622s > 622s > 622s > par(mar=c(2,3,0.2,1)+0.1) 622s > 622s > 622s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 622s > # Single-chromosome segmentation 622s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 622s > # Segment without weights 622s > fit <- segmentByCBS(data) 622s > sampleName(fit) <- "CBS_Example" 622s > print(fit) 622s sampleName chromosome start end nbrOfLoci mean 622s 1 CBS_Example 1 6.066868e+02 19076007 199 0.2622 622s 2 CBS_Example 1 1.907601e+07 29630949 99 1.4289 622s 3 CBS_Example 1 2.963095e+07 63224332 299 0.2854 622s 4 CBS_Example 1 6.322433e+07 78801707 153 -0.7408 622s 5 CBS_Example 1 7.880171e+07 99917418 199 0.3541 622s > plotTracks(fit) 622s Warning message: 622s In plotTracks.CBS(fit) : 622s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit) is unknown ('NA'). Use signalType(fit) <- 'ratio' to avoid this warning. 622s > ## Highlight outliers (they pull up the mean levels) 622s > points(x[outliers]/1e6, y[outliers], col="purple") 622s > 622s > # Segment with weights 622s > fitW <- segmentByCBS(dataW) 622s > sampleName(fitW) <- "CBS_Example (weighted)" 622s > print(fitW) 622s sampleName chromosome start end nbrOfLoci mean 622s 1 CBS_Example (weighted) 1 6.066868e+02 19076007 199 -0.0610 622s 2 CBS_Example (weighted) 1 1.907601e+07 30126128 101 1.1283 622s 3 CBS_Example (weighted) 1 3.012613e+07 63224332 297 -0.0298 622s 4 CBS_Example (weighted) 1 6.322433e+07 78801707 153 -1.0436 622s 5 CBS_Example (weighted) 1 7.880171e+07 99917418 199 0.0461 622s > drawLevels(fitW, col="red") 622s NULL 622s > 622s > legend("topright", bg="white", legend=c("outliers", "non-weighted CBS", "weighted CBS"), col=c("purple", "purple", "red"), lwd=c(NA,3,3), pch=c(1,NA,NA)) 622s > 622s > ## Assert that weighted segment means are less biased 622s > dmean <- getSegments(fit)$mean - getSegments(fitW)$mean 622s > cat("Segment mean differences:\n") 622s Segment mean differences: 622s > print(dmean) 622s [1] 0.3232 0.3006 0.3152 0.3028 0.3080 622s > stopifnot(all(dmean > 0, na.rm=TRUE)) 622s > 622s > 622s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 622s > # Segmentation with some known change points 622s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 622s > knownSegments <- data.frame( 622s + chromosome=c( 1, 1), 622s + start =x[c( 1, 401)], 622s + end =x[c(349, J)] 622s + ) 622s > fit2 <- segmentByCBS(dataW, knownSegments=knownSegments, verbose=TRUE) 622s Segmenting by CBS... 622s Chromosome: 1 622s Segmenting by CBS...done 622s > sampleName(fit2) <- "CBS_Example_2 (weighted)" 622s > print(fit2) 622s sampleName chromosome start end nbrOfLoci mean 622s 1 CBS_Example_2 (weighted) 1 6.066868e+02 19076007 199 -0.0610 622s 2 CBS_Example_2 (weighted) 1 1.907601e+07 30126128 101 1.1283 622s 3 CBS_Example_2 (weighted) 1 3.012613e+07 35490554 49 -0.0832 622s 4 CBS_Example_2 (weighted) 1 3.987525e+07 63224332 248 -0.0192 622s 5 CBS_Example_2 (weighted) 1 6.322433e+07 78471531 152 -1.0480 622s 6 CBS_Example_2 (weighted) 1 7.847153e+07 99917418 200 0.0427 622s > plotTracks(fit2) 622s Warning message: 622s In plotTracks.CBS(fit2) : 622s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit2) is unknown ('NA'). Use signalType(fit2) <- 'ratio' to avoid this warning. 622s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 622s > 622s > 622s > # Chromosome boundaries can be specified as -Inf and +Inf 622s > knownSegments <- data.frame( 622s + chromosome=c( 1, 1), 622s + start =c( -Inf, x[401]), 622s + end =c(x[349], +Inf) 622s + ) 622s > fit2b <- segmentByCBS(dataW, knownSegments=knownSegments, verbose=TRUE) 622s Segmenting by CBS... 622s Chromosome: 1 622s Segmenting by CBS...done 622s > sampleName(fit2b) <- "CBS_Example_2b (weighted)" 622s > print(fit2b) 622s sampleName chromosome start end nbrOfLoci mean 622s 1 CBS_Example_2b (weighted) 1 6.066868e+02 19076007 199 -0.0610 622s 2 CBS_Example_2b (weighted) 1 1.907601e+07 30126128 101 1.1283 622s 3 CBS_Example_2b (weighted) 1 3.012613e+07 35490554 49 -0.0832 622s 4 CBS_Example_2b (weighted) 1 3.987525e+07 63224332 248 -0.0192 622s 5 CBS_Example_2b (weighted) 1 6.322433e+07 78471531 152 -1.0480 622s 6 CBS_Example_2b (weighted) 1 7.847153e+07 99917418 200 0.0427 622s > plotTracks(fit2b) 622s Warning message: 622s In plotTracks.CBS(fit2b) : 622s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit2b) is unknown ('NA'). Use signalType(fit2b) <- 'ratio' to avoid this warning. 622s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 622s > 622s > 622s > # As a proof of concept, it is possible to segment just the centromere, 622s > # which contains no data. All statistics will be NAs. 622s > knownSegments <- data.frame( 622s + chromosome=c( 1), 622s + start =x[c(350)], 622s + end =x[c(400)] 622s + ) 622s > fit3 <- segmentByCBS(dataW, knownSegments=knownSegments, verbose=TRUE) 622s Segmenting by CBS... 622s Chromosome: 1 622s Segmenting by CBS...done 622s > sampleName(fit3) <- "CBS_Example_3" 622s > print(fit3) 622s sampleName chromosome start end nbrOfLoci mean 622s 1 CBS_Example_3 1 35661013 39852333 0 NA 622s > plotTracks(fit3, Clim=c(0,5), xlim=c(0,100)) 622s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 622s > 622s > 622s > # If one specify the (empty) centromere as a segment, then its 622s > # estimated statistics will be NAs, which becomes a natural 622s > # separator between the two "independent" arms. 622s > knownSegments <- data.frame( 622s + chromosome=c( 1, 1, 1), 622s + start =x[c( 1, 350, 401)], 622s + end =x[c(349, 400, J)] 622s + ) 622s > fit4 <- segmentByCBS(dataW, knownSegments=knownSegments, verbose=TRUE) 622s Segmenting by CBS... 622s Chromosome: 1 622s Segmenting by CBS...done 622s > sampleName(fit4) <- "CBS_Example_4" 622s > print(fit4) 622s sampleName chromosome start end nbrOfLoci mean 622s 1 CBS_Example_4 1 6.066868e+02 19076007 199 -0.0610 622s 2 CBS_Example_4 1 1.907601e+07 30126128 101 1.1283 622s 3 CBS_Example_4 1 3.012613e+07 35490554 49 -0.0832 622s 4 CBS_Example_4 1 3.566101e+07 39852333 0 NA 622s 5 CBS_Example_4 1 3.987525e+07 63224332 248 -0.0192 622s 6 CBS_Example_4 1 6.322433e+07 78471531 152 -1.0480 622s 7 CBS_Example_4 1 7.847153e+07 99917418 200 0.0427 622s > plotTracks(fit4) 622s Warning message: 622s In plotTracks.CBS(fit4) : 622s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit4) is unknown ('NA'). Use signalType(fit4) <- 'ratio' to avoid this warning. 622s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 622s > 622s > 622s > fit5 <- segmentByCBS(dataW, knownSegments=knownSegments, undo=Inf, verbose=TRUE) 622s Segmenting by CBS... 622s Chromosome: 1 622s Segmenting by CBS...done 622s > sampleName(fit5) <- "CBS_Example_5" 622s > print(fit5) 622s sampleName chromosome start end nbrOfLoci mean 622s 1 CBS_Example_5 1 6.066868e+02 35490554 349 0.59252133 622s 2 CBS_Example_5 1 3.566101e+07 39852333 0 NA 622s 3 CBS_Example_5 1 3.987525e+07 99917418 600 0.04882396 622s > plotTracks(fit5) 622s Warning message: 622s In plotTracks.CBS(fit5) : 622s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit5) is unknown ('NA'). Use signalType(fit5) <- 'ratio' to avoid this warning. 622s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 622s > stopifnot(nbrOfSegments(fit5) == nrow(knownSegments)) 622s > 622s > 622s > # One can also force a separator between two segments by setting 622s > # 'start' and 'end' to NAs ('chromosome' has to be given) 622s > knownSegments <- data.frame( 622s + chromosome=c( 1, 1, 1), 622s + start =x[c( 1, NA, 401)], 622s + end =x[c(349, NA, J)] 622s + ) 622s > fit6 <- segmentByCBS(dataW, knownSegments=knownSegments, verbose=TRUE) 622s Segmenting by CBS... 622s Chromosome: 1 622s Segmenting by CBS...done 622s > sampleName(fit6) <- "CBS_Example_6" 622s > print(fit6) 622s sampleName chromosome start end nbrOfLoci mean 622s 1 CBS_Example_6 1 6.066868e+02 19076007 199 -0.0610 622s 2 CBS_Example_6 1 1.907601e+07 30126128 101 1.1283 622s 3 CBS_Example_6 1 3.012613e+07 35490554 49 -0.0832 622s 4 NA NA NA NA NA 622s 5 CBS_Example_6 1 3.987525e+07 63224332 248 -0.0192 622s 6 CBS_Example_6 1 6.322433e+07 78471531 152 -1.0480 622s 7 CBS_Example_6 1 7.847153e+07 99917418 200 0.0427 622s > plotTracks(fit6) 622s Warning message: 622s In plotTracks.CBS(fit6) : 622s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit6) is unknown ('NA'). Use signalType(fit6) <- 'ratio' to avoid this warning. 622s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 622s > 622s > 622s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 622s > # Multi-chromosome segmentation 622s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 622s > data2 <- data 622s > data2$chromosome <- 2L 622s > data <- rbind(data, data2) 622s > dataW <- cbind(data, w=w) 622s > 622s > par(mar=c(2,3,0.2,1)+0.1) 622s > # Segment without weights 622s > fit <- segmentByCBS(data) 622s > sampleName(fit) <- "CBS_Example" 622s > print(fit) 622s sampleName chromosome start end nbrOfLoci mean 622s 1 CBS_Example 1 6.066868e+02 19076007 199 0.2622 622s 2 CBS_Example 1 1.907601e+07 29630949 99 1.4289 622s 3 CBS_Example 1 2.963095e+07 63224332 299 0.2854 622s 4 CBS_Example 1 6.322433e+07 78801707 153 -0.7408 622s 5 CBS_Example 1 7.880171e+07 99917418 199 0.3541 622s 6 NA NA NA NA NA 622s 7 CBS_Example 2 6.066868e+02 19076007 199 0.2622 622s 8 CBS_Example 2 1.907601e+07 29630949 99 1.4289 622s 9 CBS_Example 2 2.963095e+07 63224332 299 0.2854 622s 10 CBS_Example 2 6.322433e+07 78801707 153 -0.7408 622s 11 CBS_Example 2 7.880171e+07 99917418 199 0.3541 622s > plotTracks(fit, Clim=c(-3,3)) 622s > 622s > # Segment with weights 622s > fitW <- segmentByCBS(dataW) 622s > sampleName(fitW) <- "CBS_Example (weighted)" 622s > print(fitW) 622s sampleName chromosome start end nbrOfLoci mean 622s 1 CBS_Example (weighted) 1 6.066868e+02 19076007 199 -0.0610 622s 2 CBS_Example (weighted) 1 1.907601e+07 30126128 101 1.1283 622s 3 CBS_Example (weighted) 1 3.012613e+07 63224332 297 -0.0298 622s 4 CBS_Example (weighted) 1 6.322433e+07 78801707 153 -1.0436 622s 5 CBS_Example (weighted) 1 7.880171e+07 99917418 199 0.0461 622s 6 NA NA NA NA NA 622s 7 CBS_Example (weighted) 2 6.066868e+02 19076007 199 -0.0610 622s 8 CBS_Example (weighted) 2 1.907601e+07 30126128 101 1.1283 622s 9 CBS_Example (weighted) 2 3.012613e+07 63224332 297 -0.0298 622s 10 CBS_Example (weighted) 2 6.322433e+07 78801707 153 -1.0436 622s 11 CBS_Example (weighted) 2 7.880171e+07 99917418 199 0.0461 622s > drawLevels(fitW, col="red") 622s NULL 622s > 622s > legend("topright", bg="white", legend=c("outliers", "non-weighted CBS", "weighted CBS"), col=c("purple", "purple", "red"), lwd=c(NA,3,3), pch=c(1,NA,NA)) 622s > 622s > ## Assert that weighted segment means are less biased 622s > dmean <- getSegments(fit)$mean - getSegments(fitW)$mean 622s > cat("Segment mean differences:\n") 622s Segment mean differences: 622s > print(dmean) 622s [1] 0.3232 0.3006 0.3152 0.3028 0.3080 NA 0.3232 0.3006 0.3152 0.3028 622s [11] 0.3080 622s > stopifnot(all(dmean > 0, na.rm=TRUE)) 622s > 622s > proc.time() 622s user system elapsed 622s 15.763 0.714 16.466 622s Test segmentByCBS,weights passed 622s 0 622s Begin test segmentByCBS 622s + [ 0 != 0 ] 622s + echo Test segmentByCBS,weights passed 622s + echo 0 622s + echo Begin test segmentByCBS 622s + exitcode=0 622s + R CMD BATCH segmentByCBS.R 636s + cat segmentByCBS.Rout 636s 636s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 636s Copyright (C) 2024 The R Foundation for Statistical Computing 636s Platform: aarch64-unknown-linux-gnu (64-bit) 636s 636s R is free software and comes with ABSOLUTELY NO WARRANTY. 636s You are welcome to redistribute it under certain conditions. 636s Type 'license()' or 'licence()' for distribution details. 636s 636s R is a collaborative project with many contributors. 636s Type 'contributors()' for more information and 636s 'citation()' on how to cite R or R packages in publications. 636s 636s Type 'demo()' for some demos, 'help()' for on-line help, or 636s 'help.start()' for an HTML browser interface to help. 636s Type 'q()' to quit R. 636s 636s [Previously saved workspace restored] 636s 636s > ########################################################### 636s > # This tests: 636s > # - segmentByCBS(...) 636s > # - segmentByCBS(..., knownSegments) 636s > # - tileChromosomes() 636s > # - plotTracks() 636s > ########################################################### 636s > library("PSCBS") 636s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 636s 636s Attaching package: 'PSCBS' 636s 636s The following objects are masked from 'package:base': 636s 636s append, load 636s 636s > subplots <- R.utils::subplots 636s > 636s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 636s > # Simulating copy-number data 636s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 636s > set.seed(0xBEEF) 636s > 636s > # Number of loci 636s > J <- 1000 636s > 636s > mu <- double(J) 636s > mu[200:300] <- mu[200:300] + 1 636s > mu[350:400] <- NA # centromere 636s > mu[650:800] <- mu[650:800] - 1 636s > eps <- rnorm(J, sd=1/2) 636s > y <- mu + eps 636s > x <- sort(runif(length(y), max=length(y))) * 1e5 636s > w <- runif(J) 636s > w[650:800] <- 0.001 636s > 636s > 636s > subplots(8, ncol=1L) 636s > par(mar=c(1.7,1,0.2,1)+0.1) 636s > 636s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 636s > # Segmentation 636s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 636s > fit <- segmentByCBS(y, x=x) 636s > sampleName(fit) <- "CBS_Example" 636s > print(fit) 636s sampleName chromosome start end nbrOfLoci mean 636s 1 CBS_Example 0 65285.65 19648927 200 0.0109 636s 2 CBS_Example 0 19648927.46 28239656 95 0.9529 636s 3 CBS_Example 0 28239655.99 65697742 302 -0.0126 636s 4 CBS_Example 0 65697742.20 79729368 153 -0.9534 636s 5 CBS_Example 0 79729368.34 99819310 199 -0.0497 636s > plotTracks(fit) 636s Warning message: 636s In plotTracks.CBS(fit) : 636s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit) is unknown ('NA'). Use signalType(fit) <- 'ratio' to avoid this warning. 636s > 636s > 636s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 636s > # Segmentation with some known change points 636s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 636s > knownSegments <- data.frame( 636s + chromosome=c( 0, 0), 636s + start =x[c( 1, 401)], 636s + end =x[c(349, J)] 636s + ) 636s > fit2 <- segmentByCBS(y, x=x, knownSegments=knownSegments, verbose=TRUE) 636s Segmenting by CBS... 636s Chromosome: 0 636s Segmenting by CBS...done 636s > sampleName(fit2) <- "CBS_Example_2" 636s > print(fit2) 636s sampleName chromosome start end nbrOfLoci mean 636s 1 CBS_Example_2 0 65285.65 19648927 200 0.0109 636s 2 CBS_Example_2 0 19648927.46 28239656 95 0.9529 636s 3 CBS_Example_2 0 28239655.99 33106633 54 0.1169 636s 4 CBS_Example_2 0 38076667.59 65697742 248 -0.0408 636s 5 CBS_Example_2 0 65697742.20 79729368 153 -0.9534 636s 6 CBS_Example_2 0 79729368.34 99819310 199 -0.0497 636s > plotTracks(fit2) 636s Warning message: 636s In plotTracks.CBS(fit2) : 636s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit2) is unknown ('NA'). Use signalType(fit2) <- 'ratio' to avoid this warning. 636s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 636s > 636s > 636s > # Chromosome boundaries can be specified as -Inf and +Inf 636s > knownSegments <- data.frame( 636s + chromosome=c( 0, 0), 636s + start =c( -Inf, x[401]), 636s + end =c(x[349], +Inf) 636s + ) 636s > fit2b <- segmentByCBS(y, x=x, knownSegments=knownSegments, verbose=TRUE) 636s Segmenting by CBS... 636s Chromosome: 0 636s Segmenting by CBS...done 636s > sampleName(fit2b) <- "CBS_Example_2b" 636s > print(fit2b) 636s sampleName chromosome start end nbrOfLoci mean 636s 1 CBS_Example_2b 0 65285.65 19648927 200 0.0109 636s 2 CBS_Example_2b 0 19648927.46 28239656 95 0.9529 636s 3 CBS_Example_2b 0 28239655.99 33106633 54 0.1169 636s 4 CBS_Example_2b 0 38076667.59 65697742 248 -0.0408 636s 5 CBS_Example_2b 0 65697742.20 79729368 153 -0.9534 636s 6 CBS_Example_2b 0 79729368.34 99819310 199 -0.0497 636s > plotTracks(fit2b) 636s Warning message: 636s In plotTracks.CBS(fit2b) : 636s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit2b) is unknown ('NA'). Use signalType(fit2b) <- 'ratio' to avoid this warning. 636s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 636s > 636s > 636s > # As a proof of concept, it is possible to segment just the centromere, 636s > # which contains no data. All statistics will be NAs. 636s > knownSegments <- data.frame( 636s + chromosome=c( 0), 636s + start =x[c(350)], 636s + end =x[c(400)] 636s + ) 636s > fit3 <- segmentByCBS(y, x=x, knownSegments=knownSegments, verbose=TRUE) 636s Segmenting by CBS... 636s Chromosome: 0 636s Segmenting by CBS...done 636s > sampleName(fit3) <- "CBS_Example_3" 636s > print(fit3) 636s sampleName chromosome start end nbrOfLoci mean 636s 1 CBS_Example_3 0 33248518 37640521 0 NA 636s > plotTracks(fit3, Clim=c(0,5), xlim=c(0,100)) 636s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 636s > 636s > 636s > 636s > # If one specify the (empty) centromere as a segment, then its 636s > # estimated statistics will be NAs, which becomes a natural 636s > # separator between the two "independent" arms. 636s > knownSegments <- data.frame( 636s + chromosome=c( 0, 0, 0), 636s + start =x[c( 1, 350, 401)], 636s + end =x[c(349, 400, J)] 636s + ) 636s > fit4 <- segmentByCBS(y, x=x, knownSegments=knownSegments, verbose=TRUE) 636s Segmenting by CBS... 636s Chromosome: 0 636s Segmenting by CBS...done 636s > sampleName(fit4) <- "CBS_Example_4" 636s > print(fit4) 636s sampleName chromosome start end nbrOfLoci mean 636s 1 CBS_Example_4 0 65285.65 19648927 200 0.0109 636s 2 CBS_Example_4 0 19648927.46 28239656 95 0.9529 636s 3 CBS_Example_4 0 28239655.99 33106633 54 0.1169 636s 4 CBS_Example_4 0 33248517.78 37640521 0 NA 636s 5 CBS_Example_4 0 38076667.59 65697742 248 -0.0408 636s 6 CBS_Example_4 0 65697742.20 79729368 153 -0.9534 636s 7 CBS_Example_4 0 79729368.34 99819310 199 -0.0497 636s > plotTracks(fit4) 636s Warning message: 636s In plotTracks.CBS(fit4) : 636s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit4) is unknown ('NA'). Use signalType(fit4) <- 'ratio' to avoid this warning. 636s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 636s > 636s > 636s > 636s > fit5 <- segmentByCBS(y, x=x, knownSegments=knownSegments, undo=Inf, verbose=TRUE) 636s Segmenting by CBS... 636s Chromosome: 0 636s Segmenting by CBS...done 636s > sampleName(fit5) <- "CBS_Example_5" 636s > print(fit5) 636s sampleName chromosome start end nbrOfLoci mean 636s 1 CBS_Example_5 0 65285.65 33106633 349 0.2836973 636s 2 CBS_Example_5 0 33248517.78 37640521 0 NA 636s 3 CBS_Example_5 0 38076667.59 99819310 600 -0.2764472 636s > plotTracks(fit5) 636s Warning message: 636s In plotTracks.CBS(fit5) : 636s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit5) is unknown ('NA'). Use signalType(fit5) <- 'ratio' to avoid this warning. 636s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 636s > stopifnot(nbrOfSegments(fit5) == nrow(knownSegments)) 636s > 636s > 636s > # One can also force a separator between two segments by setting 636s > # 'start' and 'end' to NAs ('chromosome' has to be given) 636s > knownSegments <- data.frame( 636s + chromosome=c( 0, 0, 0), 636s + start =x[c( 1, NA, 401)], 636s + end =x[c(349, NA, J)] 636s + ) 636s > fit6 <- segmentByCBS(y, x=x, knownSegments=knownSegments, verbose=TRUE) 636s Segmenting by CBS... 636s Chromosome: 0 636s Segmenting by CBS...done 636s > sampleName(fit6) <- "CBS_Example_6" 636s > print(fit6) 636s sampleName chromosome start end nbrOfLoci mean 636s 1 CBS_Example_6 0 65285.65 19648927 200 0.0109 636s 2 CBS_Example_6 0 19648927.46 28239656 95 0.9529 636s 3 CBS_Example_6 0 28239655.99 33106633 54 0.1169 636s 4 NA NA NA NA NA 636s 5 CBS_Example_6 0 38076667.59 65697742 248 -0.0408 636s 6 CBS_Example_6 0 65697742.20 79729368 153 -0.9534 636s 7 CBS_Example_6 0 79729368.34 99819310 199 -0.0497 636s > plotTracks(fit6) 636s Warning message: 636s In plotTracks.CBS(fit6) : 636s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit6) is unknown ('NA'). Use signalType(fit6) <- 'ratio' to avoid this warning. 636s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 636s > 636s > 636s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 636s > # Segment multiple chromosomes 636s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 636s > # Simulate multiple chromosomes 636s > fit1 <- renameChromosomes(fit, from=0, to=1) 636s > fit2 <- renameChromosomes(fit, from=0, to=2) 636s > fitM <- c(fit1, fit2) 636s > fitM <- segmentByCBS(fitM) 636s > sampleName(fitM) <- "CBS_Example_M" 636s > print(fitM) 636s sampleName chromosome start end nbrOfLoci mean 636s 1 CBS_Example_M 1 65285.65 19648927 200 0.0109 636s 2 CBS_Example_M 1 19648927.46 28239656 95 0.9529 636s 3 CBS_Example_M 1 28239655.99 65697742 302 -0.0126 636s 4 CBS_Example_M 1 65697742.20 79729368 153 -0.9534 636s 5 CBS_Example_M 1 79729368.34 99819310 199 -0.0497 636s 6 NA NA NA NA NA 636s 7 CBS_Example_M 2 65285.65 19648927 200 0.0109 636s 8 CBS_Example_M 2 19648927.46 28239656 95 0.9529 636s 9 CBS_Example_M 2 28239655.99 65697742 302 -0.0126 636s 10 CBS_Example_M 2 65697742.20 79729368 153 -0.9534 636s 11 CBS_Example_M 2 79729368.34 99819310 199 -0.0497 636s > plotTracks(fitM, Clim=c(-3,3)) 636s > 636s > 636s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 636s > # Tiling multiple chromosomes 636s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 636s > # Tile chromosomes 636s > fitT <- tileChromosomes(fitM) 636s > fitTb <- tileChromosomes(fitT) 636s > stopifnot(identical(fitTb, fitT)) 636s > 636s > 636s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 636s > # Write segmentation to file 636s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 636s > pathT <- tempdir() 636s > 636s > ## Tab-delimited file 636s > pathname <- writeSegments(fitM, path=pathT) 636s Warning message: 636s In write.table(file = pathnameT, data, append = TRUE, quote = FALSE, : 636s appending column names to file 636s > print(pathname) 636s [1] "/tmp/Rtmp7jkdpq/CBS_Example_M.tsv" 636s > 636s > ## WIG file 636s > pathname <- writeWIG(fitM, path=pathT) 636s > print(pathname) 636s [1] "/tmp/Rtmp7jkdpq/CBS_Example_M.wig" 636s > 636s > unlink(pathT, recursive=TRUE) 636s > 636s > proc.time() 636s user system elapsed 636s 12.809 0.572 13.354 637s Test segmentByCBS passed 637s 0 637s Begin test segmentByNonPairedPSCBS,medianDH 637s + [ 0 != 0 ] 637s + echo Test segmentByCBS passed 637s + echo 0 637s + echo Begin test segmentByNonPairedPSCBS,medianDH 637s + exitcode=0 637s + R CMD BATCH segmentByNonPairedPSCBS,medianDH.R 651s + cat segmentByNonPairedPSCBS,medianDH.Rout 651s 651s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 651s Copyright (C) 2024 The R Foundation for Statistical Computing 651s Platform: aarch64-unknown-linux-gnu (64-bit) 651s 651s R is free software and comes with ABSOLUTELY NO WARRANTY. 651s You are welcome to redistribute it under certain conditions. 651s Type 'license()' or 'licence()' for distribution details. 651s 651s R is a collaborative project with many contributors. 651s Type 'contributors()' for more information and 651s 'citation()' on how to cite R or R packages in publications. 651s 651s Type 'demo()' for some demos, 'help()' for on-line help, or 651s 'help.start()' for an HTML browser interface to help. 651s Type 'q()' to quit R. 651s 651s [Previously saved workspace restored] 651s 651s > library("PSCBS") 651s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 651s 651s Attaching package: 'PSCBS' 651s 651s The following objects are masked from 'package:base': 651s 651s append, load 651s 651s > 651s > 651s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 651s > # Load SNP microarray data 651s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 651s > data <- PSCBS::exampleData("paired.chr01") 651s > str(data) 651s 'data.frame': 73346 obs. of 6 variables: 651s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 651s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 651s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 651s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 651s $ CN : num 2.36 2.13 2.59 1.93 1.71 ... 651s $ betaN : num 0.827 0.875 0.887 0.884 0.103 ... 651s > 651s > # Non-paired / tumor-only data 651s > data <- data[,c("chromosome", "x", "CT", "betaT")] 651s > str(data) 651s 'data.frame': 73346 obs. of 4 variables: 651s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 651s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 651s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 651s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 651s > 651s > 651s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 651s > # Paired PSCBS segmentation 651s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 651s > # Drop single-locus outliers 651s > dataS <- dropSegmentationOutliers(data) 651s > 651s > # Speed up example by segmenting fewer loci 651s > dataS <- dataS[seq(from=1, to=nrow(data), by=20),] 651s > 651s > # Fake a second chromosome 651s > dataT <- dataS 651s > dataT$chromosome <- 2L 651s > dataS <- rbind(dataS, dataT) 651s > rm(dataT) 651s > str(dataS) 651s 'data.frame': 7336 obs. of 4 variables: 651s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 651s $ x : int 1145994 4276892 5034491 6266412 8418532 11211748 13928296 14370144 15014887 16589707 ... 651s $ CT : num 1.63 1.16 1.35 1.39 1.55 ... 651s $ betaT : num 0.7574 0.0576 0.8391 0.7917 0.8141 ... 651s > 651s > # Non-Paired PSCBS segmentation 651s > fit <- segmentByNonPairedPSCBS(dataS, avgDH="median", seed=0xBEEF, verbose=-10) 651s Segmenting non-paired tumor signals using Non-paired PSCBS... 651s Number of loci: 7336 651s Number of SNPs: 7336 651s Calling "genotypes" from tumor allele B fractions... 651s num [1:7336] 0.7574 0.0576 0.8391 0.7917 0.8141 ... 651s Upper quantile: 0.475631667925522 651s Symmetric lower quantile: 0.290517384533512 651s (tauA, tauB) estimates: (%g,%g)0.2094826154664880.790517384533512 651s Homozygous treshholds: 651s [1] 0.2094826 0.7905174 651s Inferred germline genotypes (via tumor): 651s num [1:7336] 0.5 0 1 1 1 0 0 0 0.5 1 ... 651s muNx 651s 0 0.5 1 651s 2230 2910 2196 651s Calling "genotypes" from tumor allele B fractions...done 651s Segmenting non-paired tumor signals using Non-paired PSCBS...done 651s Segment using Paired PSCBS... 651s Segmenting paired tumor-normal signals using Paired PSCBS... 651s Setup up data... 651s 'data.frame': 7336 obs. of 6 variables: 651s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 651s $ x : num 1145994 4276892 5034491 6266412 8418532 ... 651s $ CT : num 1.63 1.16 1.35 1.39 1.55 ... 651s $ betaT : num 0.7574 0.0576 0.8391 0.7917 0.8141 ... 651s $ betaTN : num 0.7574 0.0576 0.8391 0.7917 0.8141 ... 651s $ muN : num 0.5 0 1 1 1 0 0 0 0.5 1 ... 651s Setup up data...done 651s Dropping loci for which TCNs are missing... 651s Number of loci dropped: 12 651s Dropping loci for which TCNs are missing...done 651s Ordering data along genome... 651s 'data.frame': 7324 obs. of 6 variables: 651s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 651s $ x : num 554484 1031563 1087198 1145994 1176365 ... 651s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 651s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 651s Ordering data along genome...done 651s Segmenting multiple chromosomes... 651s Number of chromosomes: 2 651s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 651s Produced 2 seeds from this stream for future usage 651s Chromosome #1 ('Chr01') of 2... 651s 'data.frame': 3662 obs. of 7 variables: 651s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 651s $ x : num 554484 1031563 1087198 1145994 1176365 ... 651s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 651s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 651s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 651s Known segments: 651s [1] chromosome start end 651s <0 rows> (or 0-length row.names) 651s Segmenting paired tumor-normal signals using Paired PSCBS... 651s Setup up data... 651s 'data.frame': 3662 obs. of 6 variables: 651s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 651s $ x : num 554484 1031563 1087198 1145994 1176365 ... 651s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 651s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 651s Setup up data...done 651s Ordering data along genome... 651s 'data.frame': 3662 obs. of 6 variables: 651s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 651s $ x : num 554484 1031563 1087198 1145994 1176365 ... 651s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 651s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 651s Ordering data along genome...done 651s Keeping only current chromosome for 'knownSegments'... 651s Chromosome: 1 651s Known segments for this chromosome: 651s [1] chromosome start end 651s <0 rows> (or 0-length row.names) 651s Keeping only current chromosome for 'knownSegments'...done 651s alphaTCN: 0.009 651s alphaDH: 0.001 651s Number of loci: 3662 651s Calculating DHs... 651s Number of SNPs: 3662 651s Number of heterozygous SNPs: 1451 (39.62%) 651s Normalized DHs: 651s num [1:3662] NA 0.216 0.198 0.515 0.29 ... 651s Calculating DHs...done 651s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 651s Produced 2 seeds from this stream for future usage 651s Identification of change points by total copy numbers... 651s Segmenting by CBS... 651s Chromosome: 1 651s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 651s Segmenting by CBS...done 651s List of 4 651s $ data :'data.frame': 3662 obs. of 4 variables: 651s ..$ chromosome: int [1:3662] 1 1 1 1 1 1 1 1 1 1 ... 651s ..$ x : num [1:3662] 554484 1031563 1087198 1145994 1176365 ... 651s ..$ y : num [1:3662] 1.88 1.64 1.77 1.63 1.59 ... 651s ..$ index : int [1:3662] 1 2 3 4 5 6 7 8 9 10 ... 651s $ output :'data.frame': 3 obs. of 6 variables: 651s ..$ sampleName: chr [1:3] NA NA NA 651s ..$ chromosome: int [1:3] 1 1 1 651s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 651s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 651s ..$ nbrOfLoci : int [1:3] 1880 671 1111 651s ..$ mean : num [1:3] 1.39 2.09 2.65 651s $ segRows:'data.frame': 3 obs. of 2 variables: 651s ..$ startRow: int [1:3] 1 1881 2552 651s ..$ endRow : int [1:3] 1880 2551 3662 651s $ params :List of 5 651s ..$ alpha : num 0.009 651s ..$ undo : num 0 651s ..$ joinSegments : logi TRUE 651s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 651s .. ..$ chromosome: int 1 651s .. ..$ start : num -Inf 651s .. ..$ end : num Inf 651s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 651s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 651s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.309 0.003 0.312 0 0 651s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 651s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 651s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 651s Identification of change points by total copy numbers...done 651s Restructure TCN segmentation results... 651s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 651s 1 1 554484 143663981 1880 1.3916 651s 2 1 143663981 185240536 671 2.0925 651s 3 1 185240536 246679946 1111 2.6545 651s Number of TCN segments: 3 651s Restructure TCN segmentation results...done 651s TCN-only segmentation... 651s Total CN segment #1 ([ 554484,1.43664e+08]) of 3... 651s Number of TCN loci in segment: 1880 651s Locus data for TCN segment: 651s 'data.frame': 1880 obs. of 8 variables: 651s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 651s $ x : num 554484 1031563 1087198 1145994 1176365 ... 651s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 651s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 651s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 651s $ rho : num NA 0.216 0.198 0.515 0.29 ... 651s Number of loci: 1880 651s Number of SNPs: 765 (40.69%) 651s Number of heterozygous SNPs: 765 (100.00%) 651s Total CN segment #1 ([ 554484,1.43664e+08]) of 3...done 651s Total CN segment #2 ([1.43664e+08,1.85241e+08]) of 3... 651s Number of TCN loci in segment: 671 651s Locus data for TCN segment: 651s 'data.frame': 671 obs. of 8 variables: 651s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 651s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 651s $ CT : num 2.26 2.1 2.1 1.89 1.97 ... 651s $ betaT : num 0.958 0.19 0.909 0.13 0.141 ... 651s $ betaTN : num 0.958 0.19 0.909 0.13 0.141 ... 651s $ muN : num 1 0 1 0 0 0 0 0.5 0 1 ... 651s $ index : int 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 ... 651s $ rho : num NA NA NA NA NA ... 651s Number of loci: 671 651s Number of SNPs: 272 (40.54%) 651s Number of heterozygous SNPs: 272 (100.00%) 651s Total CN segment #2 ([1.43664e+08,1.85241e+08]) of 3...done 651s Total CN segment #3 ([1.85241e+08,2.4668e+08]) of 3... 651s Number of TCN loci in segment: 1111 651s Locus data for TCN segment: 651s 'data.frame': 1111 obs. of 8 variables: 651s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 651s $ x : num 1.85e+08 1.86e+08 1.86e+08 1.86e+08 1.86e+08 ... 651s $ CT : num 2.44 3 2.32 2.76 2.48 ... 651s $ betaT : num 0.0727 0.6845 0.2327 0.8118 0.0746 ... 651s $ betaTN : num 0.0727 0.6845 0.2327 0.8118 0.0746 ... 651s $ muN : num 0 0.5 0.5 1 0 1 0 1 1 0.5 ... 651s $ index : int 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 ... 651s $ rho : num NA 0.369 0.535 NA NA ... 651s Number of loci: 1111 651s Number of SNPs: 414 (37.26%) 651s Number of heterozygous SNPs: 414 (100.00%) 651s Total CN segment #3 ([1.85241e+08,2.4668e+08]) of 3...done 651s TCN-only segmentation...done 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 1 1 1 1 554484 143663981 1880 1.3916 765 651s 2 1 2 1 143663981 185240536 671 2.0925 272 651s 3 1 3 1 185240536 246679946 1111 2.6545 414 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean 651s 1 765 765 554484 143663981 0.3979122 651s 2 272 272 143663981 185240536 0.2306116 651s 3 414 414 185240536 246679946 0.2798120 651s Calculating (C1,C2) per segment... 651s Calculating (C1,C2) per segment...done 651s Number of segments: 3 651s Segmenting paired tumor-normal signals using Paired PSCBS...done 651s Updating mean level using different estimator... 651s TCN estimator: mean 651s DH estimator: median 651s Updating mean level using different estimator...done 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 1 1 1 1 554484 143663981 1880 1.391608 765 651s 2 1 2 1 143663981 185240536 671 2.092452 272 651s 3 1 3 1 185240536 246679946 1111 2.654512 414 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 651s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 651s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 1 1 1 1 554484 143663981 1880 1.391608 765 651s 2 1 2 1 143663981 185240536 671 2.092452 272 651s 3 1 3 1 185240536 246679946 1111 2.654512 414 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 651s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 651s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 1 1 1 1 554484 143663981 1880 1.391608 765 651s 2 1 2 1 143663981 185240536 671 2.092452 272 651s 3 1 3 1 185240536 246679946 1111 2.654512 414 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 651s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 651s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 1 1 1 1 554484 143663981 1880 1.391608 765 651s 2 1 2 1 143663981 185240536 671 2.092452 272 651s 3 1 3 1 185240536 246679946 1111 2.654512 414 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 651s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 651s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 651s Chromosome #1 ('Chr01') of 2...done 651s Chromosome #2 ('Chr02') of 2... 651s 'data.frame': 3662 obs. of 7 variables: 651s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 651s $ x : num 554484 1031563 1087198 1145994 1176365 ... 651s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 651s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 651s $ index : int 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 ... 651s Known segments: 651s [1] chromosome start end 651s <0 rows> (or 0-length row.names) 651s Segmenting paired tumor-normal signals using Paired PSCBS... 651s Setup up data... 651s 'data.frame': 3662 obs. of 6 variables: 651s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 651s $ x : num 554484 1031563 1087198 1145994 1176365 ... 651s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 651s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 651s Setup up data...done 651s Ordering data along genome... 651s 'data.frame': 3662 obs. of 6 variables: 651s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 651s $ x : num 554484 1031563 1087198 1145994 1176365 ... 651s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 651s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 651s Ordering data along genome...done 651s Keeping only current chromosome for 'knownSegments'... 651s Chromosome: 2 651s Known segments for this chromosome: 651s [1] chromosome start end 651s <0 rows> (or 0-length row.names) 651s Keeping only current chromosome for 'knownSegments'...done 651s alphaTCN: 0.009 651s alphaDH: 0.001 651s Number of loci: 3662 651s Calculating DHs... 651s Number of SNPs: 3662 651s Number of heterozygous SNPs: 1451 (39.62%) 651s Normalized DHs: 651s num [1:3662] NA 0.216 0.198 0.515 0.29 ... 651s Calculating DHs...done 651s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 651s Produced 2 seeds from this stream for future usage 651s Identification of change points by total copy numbers... 651s Segmenting by CBS... 651s Chromosome: 2 651s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 651s Segmenting by CBS...done 651s List of 4 651s $ data :'data.frame': 3662 obs. of 4 variables: 651s ..$ chromosome: int [1:3662] 2 2 2 2 2 2 2 2 2 2 ... 651s ..$ x : num [1:3662] 554484 1031563 1087198 1145994 1176365 ... 651s ..$ y : num [1:3662] 1.88 1.64 1.77 1.63 1.59 ... 651s ..$ index : int [1:3662] 1 2 3 4 5 6 7 8 9 10 ... 651s $ output :'data.frame': 3 obs. of 6 variables: 651s ..$ sampleName: chr [1:3] NA NA NA 651s ..$ chromosome: int [1:3] 2 2 2 651s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 651s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 651s ..$ nbrOfLoci : int [1:3] 1880 671 1111 651s ..$ mean : num [1:3] 1.39 2.09 2.65 651s $ segRows:'data.frame': 3 obs. of 2 variables: 651s ..$ startRow: int [1:3] 1 1881 2552 651s ..$ endRow : int [1:3] 1880 2551 3662 651s $ params :List of 5 651s ..$ alpha : num 0.009 651s ..$ undo : num 0 651s ..$ joinSegments : logi TRUE 651s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 651s .. ..$ chromosome: int 2 651s .. ..$ start : num -Inf 651s .. ..$ end : num Inf 651s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 651s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 651s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.422 0.01 0.432 0 0 651s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 651s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 651s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 651s Identification of change points by total copy numbers...done 651s Restructure TCN segmentation results... 651s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 651s 1 2 554484 143663981 1880 1.3916 651s 2 2 143663981 185240536 671 2.0925 651s 3 2 185240536 246679946 1111 2.6545 651s Number of TCN segments: 3 651s Restructure TCN segmentation results...done 651s TCN-only segmentation... 651s Total CN segment #1 ([ 554484,1.43664e+08]) of 3... 651s Number of TCN loci in segment: 1880 651s Locus data for TCN segment: 651s 'data.frame': 1880 obs. of 8 variables: 651s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 651s $ x : num 554484 1031563 1087198 1145994 1176365 ... 651s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 651s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 651s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 651s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 651s $ rho : num NA 0.216 0.198 0.515 0.29 ... 651s Number of loci: 1880 651s Number of SNPs: 765 (40.69%) 651s Number of heterozygous SNPs: 765 (100.00%) 651s Total CN segment #1 ([ 554484,1.43664e+08]) of 3...done 651s Total CN segment #2 ([1.43664e+08,1.85241e+08]) of 3... 651s Number of TCN loci in segment: 671 651s Locus data for TCN segment: 651s 'data.frame': 671 obs. of 8 variables: 651s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 651s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 651s $ CT : num 2.26 2.1 2.1 1.89 1.97 ... 651s $ betaT : num 0.958 0.19 0.909 0.13 0.141 ... 651s $ betaTN : num 0.958 0.19 0.909 0.13 0.141 ... 651s $ muN : num 1 0 1 0 0 0 0 0.5 0 1 ... 651s $ index : int 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 ... 651s $ rho : num NA NA NA NA NA ... 651s Number of loci: 671 651s Number of SNPs: 272 (40.54%) 651s Number of heterozygous SNPs: 272 (100.00%) 651s Total CN segment #2 ([1.43664e+08,1.85241e+08]) of 3...done 651s Total CN segment #3 ([1.85241e+08,2.4668e+08]) of 3... 651s Number of TCN loci in segment: 1111 651s Locus data for TCN segment: 651s 'data.frame': 1111 obs. of 8 variables: 651s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 651s $ x : num 1.85e+08 1.86e+08 1.86e+08 1.86e+08 1.86e+08 ... 651s $ CT : num 2.44 3 2.32 2.76 2.48 ... 651s $ betaT : num 0.0727 0.6845 0.2327 0.8118 0.0746 ... 651s $ betaTN : num 0.0727 0.6845 0.2327 0.8118 0.0746 ... 651s $ muN : num 0 0.5 0.5 1 0 1 0 1 1 0.5 ... 651s $ index : int 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 ... 651s $ rho : num NA 0.369 0.535 NA NA ... 651s Number of loci: 1111 651s Number of SNPs: 414 (37.26%) 651s Number of heterozygous SNPs: 414 (100.00%) 651s Total CN segment #3 ([1.85241e+08,2.4668e+08]) of 3...done 651s TCN-only segmentation...done 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 1 2 1 1 554484 143663981 1880 1.3916 765 651s 2 2 2 1 143663981 185240536 671 2.0925 272 651s 3 2 3 1 185240536 246679946 1111 2.6545 414 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean 651s 1 765 765 554484 143663981 0.3979122 651s 2 272 272 143663981 185240536 0.2306116 651s 3 414 414 185240536 246679946 0.2798120 651s Calculating (C1,C2) per segment... 651s Calculating (C1,C2) per segment...done 651s Number of segments: 3 651s Segmenting paired tumor-normal signals using Paired PSCBS...done 651s Updating mean level using different estimator... 651s TCN estimator: mean 651s DH estimator: median 651s Updating mean level using different estimator...done 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 1 2 1 1 554484 143663981 1880 1.391608 765 651s 2 2 2 1 143663981 185240536 671 2.092452 272 651s 3 2 3 1 185240536 246679946 1111 2.654512 414 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 651s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 651s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 1 2 1 1 554484 143663981 1880 1.391608 765 651s 2 2 2 1 143663981 185240536 671 2.092452 272 651s 3 2 3 1 185240536 246679946 1111 2.654512 414 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 651s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 651s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 1 2 1 1 554484 143663981 1880 1.391608 765 651s 2 2 2 1 143663981 185240536 671 2.092452 272 651s 3 2 3 1 185240536 246679946 1111 2.654512 414 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 651s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 651s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 1 2 1 1 554484 143663981 1880 1.391608 765 651s 2 2 2 1 143663981 185240536 671 2.092452 272 651s 3 2 3 1 185240536 246679946 1111 2.654512 414 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 651s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 651s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 651s Chromosome #2 ('Chr02') of 2...done 651s Merging (independently) segmented chromosome... 651s List of 5 651s $ data :Classes 'PairedPSCNData' and 'data.frame': 7324 obs. of 7 variables: 651s ..$ chromosome: int [1:7324] 1 1 1 1 1 1 1 1 1 1 ... 651s ..$ x : num [1:7324] 554484 1031563 1087198 1145994 1176365 ... 651s ..$ CT : num [1:7324] 1.88 1.64 1.77 1.63 1.59 ... 651s ..$ betaT : num [1:7324] 0.0646 0.6078 0.401 0.7574 0.645 ... 651s ..$ betaTN : num [1:7324] 0.0646 0.6078 0.401 0.7574 0.645 ... 651s ..$ muN : num [1:7324] 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 651s ..$ rho : num [1:7324] NA 0.216 0.198 0.515 0.29 ... 651s $ output :Classes 'PairedPSCNSegments' and 'data.frame': 7 obs. of 15 variables: 651s ..$ chromosome : int [1:7] 1 1 1 NA 2 2 2 651s ..$ tcnId : int [1:7] 1 2 3 NA 1 2 3 651s ..$ dhId : int [1:7] 1 1 1 NA 1 1 1 651s ..$ tcnStart : num [1:7] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... 651s ..$ tcnEnd : num [1:7] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... 651s ..$ tcnNbrOfLoci: int [1:7] 1880 671 1111 NA 1880 671 1111 651s ..$ tcnMean : num [1:7] 1.39 2.09 2.65 NA 1.39 ... 651s ..$ tcnNbrOfSNPs: int [1:7] 765 272 414 NA 765 272 414 651s ..$ tcnNbrOfHets: int [1:7] 765 272 414 NA 765 272 414 651s ..$ dhNbrOfLoci : int [1:7] 765 272 414 NA 765 272 414 651s ..$ dhStart : num [1:7] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... 651s ..$ dhEnd : num [1:7] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... 651s ..$ dhMean : num [1:7] 0.421 0.176 0.27 NA 0.421 ... 651s ..$ c1Mean : num [1:7] 0.403 0.862 0.969 NA 0.403 ... 651s ..$ c2Mean : num [1:7] 0.988 1.231 1.685 NA 0.988 ... 651s $ tcnSegRows:'data.frame': 7 obs. of 2 variables: 651s ..$ startRow: int [1:7] 1 1881 2552 NA 3663 5543 6214 651s ..$ endRow : int [1:7] 1880 2551 3662 NA 5542 6213 7324 651s $ dhSegRows :'data.frame': 7 obs. of 2 variables: 651s ..$ startRow: int [1:7] 2 1888 2553 NA 3664 5550 6215 651s ..$ endRow : int [1:7] 1876 2548 3659 NA 5538 6210 7321 651s $ params :List of 8 651s ..$ alphaTCN : num 0.009 651s ..$ alphaDH : num 0.001 651s ..$ flavor : chr "tcn" 651s ..$ tbn : logi FALSE 651s ..$ joinSegments : logi TRUE 651s ..$ knownSegments :'data.frame': 0 obs. of 3 variables: 651s .. ..$ chromosome: int(0) 651s .. ..$ start : int(0) 651s .. ..$ end : int(0) 651s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 651s ..$ meanEstimators:List of 2 651s .. ..$ tcn: chr "mean" 651s .. ..$ dh : chr "median" 651s - attr(*, "class")= chr [1:3] "PairedPSCBS" "PSCBS" "AbstractCBS" 651s Merging (independently) segmented chromosome...done 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 1 1 1 1 554484 143663981 1880 1.391608 765 651s 2 1 2 1 143663981 185240536 671 2.092452 272 651s 3 1 3 1 185240536 246679946 1111 2.654512 414 651s 4 NA NA NA NA NA NA NA NA 651s 5 2 1 1 554484 143663981 1880 1.391608 765 651s 6 2 2 1 143663981 185240536 671 2.092452 272 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 651s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 651s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 651s 4 NA NA NA NA NA NA NA 651s 5 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 651s 6 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 2 1 2 1 143663981 185240536 671 2.092452 272 651s 3 1 3 1 185240536 246679946 1111 2.654512 414 651s 4 NA NA NA NA NA NA NA NA 651s 5 2 1 1 554484 143663981 1880 1.391608 765 651s 6 2 2 1 143663981 185240536 671 2.092452 272 651s 7 2 3 1 185240536 246679946 1111 2.654512 414 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 651s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 651s 4 NA NA NA NA NA NA NA 651s 5 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 651s 6 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 651s 7 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 651s Segmenting multiple chromosomes...done 651s Segmenting paired tumor-normal signals using Paired PSCBS...done 651s Segment using Paired PSCBS...done 651s Coercing to Non-Paired PSCBS results... 651s Coercing to Non-Paired PSCBS results...done 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 1 1 1 1 554484 143663981 1880 1.391608 765 651s 2 1 2 1 143663981 185240536 671 2.092452 272 651s 3 1 3 1 185240536 246679946 1111 2.654512 414 651s 4 NA NA NA NA NA NA NA NA 651s 5 2 1 1 554484 143663981 1880 1.391608 765 651s 6 2 2 1 143663981 185240536 671 2.092452 272 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 651s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 651s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 651s 4 NA NA NA NA NA NA NA 651s 5 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 651s 6 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 2 1 2 1 143663981 185240536 671 2.092452 272 651s 3 1 3 1 185240536 246679946 1111 2.654512 414 651s 4 NA NA NA NA NA NA NA NA 651s 5 2 1 1 554484 143663981 1880 1.391608 765 651s 6 2 2 1 143663981 185240536 671 2.092452 272 651s 7 2 3 1 185240536 246679946 1111 2.654512 414 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 651s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 651s 4 NA NA NA NA NA NA NA 651s 5 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 651s 6 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 651s 7 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 651s > print(fit) 651s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 1 1 1 1 554484 143663981 1880 1.391608 765 651s 2 1 2 1 143663981 185240536 671 2.092452 272 651s 3 1 3 1 185240536 246679946 1111 2.654512 414 651s 4 NA NA NA NA NA NA NA NA 651s 5 2 1 1 554484 143663981 1880 1.391608 765 651s 6 2 2 1 143663981 185240536 671 2.092452 272 651s 7 2 3 1 185240536 246679946 1111 2.654512 414 651s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 651s 1 765 765 0.4206323 0.4031263 0.9884817 651s 2 272 272 0.1762428 0.8618360 1.2306156 651s 3 414 414 0.2697420 0.9692395 1.6852728 651s 4 NA NA NA NA NA 651s 5 765 765 0.4206323 0.4031263 0.9884817 651s 6 272 272 0.1762428 0.8618360 1.2306156 651s 7 414 414 0.2697420 0.9692395 1.6852728 651s > 651s > 651s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 651s > # Bootstrap segment level estimates 651s > # (used by the AB caller, which, if skipped here, 651s > # will do it automatically) 651s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 651s > fit <- bootstrapTCNandDHByRegion(fit, B=100, verbose=-10) 651s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint... 651s Already done? 651s tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% dh_97.5% 651s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 651s c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% c2_97.5% 651s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 651s Bootstrapping (TCN,DH,C1,C2) segment mean levels... 651s Identifying heterozygous & homozygous SNPs and non-polymorphic loci... 651s Number of loci: 7324 651s Number of SNPs: 2902 651s Number of non-SNPs: 4422 651s Identifying heterozygous & homozygous SNPs and non-polymorphic loci...done 651s num [1:7, 1:100, 1:4] NA NA NA NA NA NA NA NA NA NA ... 651s - attr(*, "dimnames")=List of 3 651s ..$ : NULL 651s ..$ : NULL 651s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 651s Segment #1 (chr 1, tcnId=1, dhId=1) of 7... 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 1 1 1 1 554484 143663981 1880 1.391608 765 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 651s Number of TCNs: 1880 651s Number of DHs: 765 651s int [1:1880] 1 2 3 4 5 6 7 8 9 10 ... 651s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 651s int [1:1880] 1 2 3 4 5 6 7 8 9 10 ... 651s Identify loci used to bootstrap DH means... 651s Heterozygous SNPs to resample for DH: 651s int [1:765] 2 3 4 5 6 8 9 10 11 12 ... 651s Identify loci used to bootstrap DH means...done 651s Identify loci used to bootstrap TCN means... 651s SNPs: 651s int [1:765] 2 3 4 5 6 8 9 10 11 12 ... 651s Non-polymorphic loci: 651s int [1:1115] 1 7 15 28 30 32 34 35 36 37 ... 651s Heterozygous SNPs to resample for TCN: 651s int [1:765] 2 3 4 5 6 8 9 10 11 12 ... 651s Homozygous SNPs to resample for TCN: 651s int(0) 651s Non-polymorphic loci to resample for TCN: 651s int [1:1115] 1 7 15 28 30 32 34 35 36 37 ... 651s Heterozygous SNPs with non-DH to resample for TCN: 651s int(0) 651s Loci to resample for TCN: 651s int [1:1880] 1 2 3 4 5 6 7 8 9 10 ... 651s Identify loci used to bootstrap TCN means...done 651s Number of (#hets, #homs, #nonSNPs): (765,0,1115) 651s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 651s Number of bootstrap samples: 100 651s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 651s Segment #1 (chr 1, tcnId=1, dhId=1) of 7...done 651s Segment #2 (chr 1, tcnId=2, dhId=1) of 7... 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 2 1 2 1 143663981 185240536 671 2.092452 272 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 2 272 272 143663981 185240536 0.1762428 0.861836 1.230616 651s Number of TCNs: 671 651s Number of DHs: 272 651s int [1:671] 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 ... 651s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 651s int [1:671] 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 ... 651s Identify loci used to bootstrap DH means... 651s Heterozygous SNPs to resample for DH: 651s int [1:272] 1888 1893 1894 1895 1896 1897 1901 1903 1907 1908 ... 651s Identify loci used to bootstrap DH means...done 651s Identify loci used to bootstrap TCN means... 651s SNPs: 651s int [1:272] 1888 1893 1894 1895 1896 1897 1901 1903 1907 1908 ... 651s Non-polymorphic loci: 651s int [1:399] 1881 1882 1883 1884 1885 1886 1887 1889 1890 1891 ... 651s Heterozygous SNPs to resample for TCN: 651s int [1:272] 1888 1893 1894 1895 1896 1897 1901 1903 1907 1908 ... 651s Homozygous SNPs to resample for TCN: 651s int(0) 651s Non-polymorphic loci to resample for TCN: 651s int [1:399] 1881 1882 1883 1884 1885 1886 1887 1889 1890 1891 ... 651s Heterozygous SNPs with non-DH to resample for TCN: 651s int(0) 651s Loci to resample for TCN: 651s int [1:671] 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 ... 651s Identify loci used to bootstrap TCN means...done 651s Number of (#hets, #homs, #nonSNPs): (272,0,399) 651s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 651s Number of bootstrap samples: 100 651s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 651s Segment #2 (chr 1, tcnId=2, dhId=1) of 7...done 651s Segment #3 (chr 1, tcnId=3, dhId=1) of 7... 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 3 1 3 1 185240536 246679946 1111 2.654512 414 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 3 414 414 185240536 246679946 0.269742 0.9692395 1.685273 651s Number of TCNs: 1111 651s Number of DHs: 414 651s int [1:1111] 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 ... 651s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 651s int [1:1111] 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 ... 651s Identify loci used to bootstrap DH means... 651s Heterozygous SNPs to resample for DH: 651s int [1:414] 2553 2554 2561 2562 2563 2568 2569 2572 2573 2574 ... 651s Identify loci used to bootstrap DH means...done 651s Identify loci used to bootstrap TCN means... 651s SNPs: 651s int [1:414] 2553 2554 2561 2562 2563 2568 2569 2572 2573 2574 ... 651s Non-polymorphic loci: 651s int [1:697] 2552 2555 2556 2557 2558 2559 2560 2564 2565 2566 ... 651s Heterozygous SNPs to resample for TCN: 651s int [1:414] 2553 2554 2561 2562 2563 2568 2569 2572 2573 2574 ... 651s Homozygous SNPs to resample for TCN: 651s int(0) 651s Non-polymorphic loci to resample for TCN: 651s int [1:697] 2552 2555 2556 2557 2558 2559 2560 2564 2565 2566 ... 651s Heterozygous SNPs with non-DH to resample for TCN: 651s int(0) 651s Loci to resample for TCN: 651s int [1:1111] 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 ... 651s Identify loci used to bootstrap TCN means...done 651s Number of (#hets, #homs, #nonSNPs): (414,0,697) 651s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 651s Number of bootstrap samples: 100 651s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 651s Segment #3 (chr 1, tcnId=3, dhId=1) of 7...done 651s Segment #5 (chr 2, tcnId=1, dhId=1) of 7... 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 5 2 1 1 554484 143663981 1880 1.391608 765 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 5 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 651s Number of TCNs: 1880 651s Number of DHs: 765 651s int [1:1880] 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 ... 651s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 651s int [1:1880] 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 ... 651s Identify loci used to bootstrap DH means... 651s Heterozygous SNPs to resample for DH: 651s int [1:765] 3664 3665 3666 3667 3668 3670 3671 3672 3673 3674 ... 651s Identify loci used to bootstrap DH means...done 651s Identify loci used to bootstrap TCN means... 651s SNPs: 651s int [1:765] 3664 3665 3666 3667 3668 3670 3671 3672 3673 3674 ... 651s Non-polymorphic loci: 651s int [1:1115] 3663 3669 3677 3690 3692 3694 3696 3697 3698 3699 ... 651s Heterozygous SNPs to resample for TCN: 651s int [1:765] 3664 3665 3666 3667 3668 3670 3671 3672 3673 3674 ... 651s Homozygous SNPs to resample for TCN: 651s int(0) 651s Non-polymorphic loci to resample for TCN: 651s int [1:1115] 3663 3669 3677 3690 3692 3694 3696 3697 3698 3699 ... 651s Heterozygous SNPs with non-DH to resample for TCN: 651s int(0) 651s Loci to resample for TCN: 651s int [1:1880] 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 ... 651s Identify loci used to bootstrap TCN means...done 651s Number of (#hets, #homs, #nonSNPs): (765,0,1115) 651s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 651s Number of bootstrap samples: 100 651s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 651s Segment #5 (chr 2, tcnId=1, dhId=1) of 7...done 651s Segment #6 (chr 2, tcnId=2, dhId=1) of 7... 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 6 2 2 1 143663981 185240536 671 2.092452 272 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 6 272 272 143663981 185240536 0.1762428 0.861836 1.230616 651s Number of TCNs: 671 651s Number of DHs: 272 651s int [1:671] 5543 5544 5545 5546 5547 5548 5549 5550 5551 5552 ... 651s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 651s int [1:671] 5543 5544 5545 5546 5547 5548 5549 5550 5551 5552 ... 651s Identify loci used to bootstrap DH means... 651s Heterozygous SNPs to resample for DH: 651s int [1:272] 5550 5555 5556 5557 5558 5559 5563 5565 5569 5570 ... 651s Identify loci used to bootstrap DH means...done 651s Identify loci used to bootstrap TCN means... 651s SNPs: 651s int [1:272] 5550 5555 5556 5557 5558 5559 5563 5565 5569 5570 ... 651s Non-polymorphic loci: 651s int [1:399] 5543 5544 5545 5546 5547 5548 5549 5551 5552 5553 ... 651s Heterozygous SNPs to resample for TCN: 651s int [1:272] 5550 5555 5556 5557 5558 5559 5563 5565 5569 5570 ... 651s Homozygous SNPs to resample for TCN: 651s int(0) 651s Non-polymorphic loci to resample for TCN: 651s int [1:399] 5543 5544 5545 5546 5547 5548 5549 5551 5552 5553 ... 651s Heterozygous SNPs with non-DH to resample for TCN: 651s int(0) 651s Loci to resample for TCN: 651s int [1:671] 5543 5544 5545 5546 5547 5548 5549 5550 5551 5552 ... 651s Identify loci used to bootstrap TCN means...done 651s Number of (#hets, #homs, #nonSNPs): (272,0,399) 651s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 651s Number of bootstrap samples: 100 651s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 651s Segment #6 (chr 2, tcnId=2, dhId=1) of 7...done 651s Segment #7 (chr 2, tcnId=3, dhId=1) of 7... 651s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 7 2 3 1 185240536 246679946 1111 2.654512 414 651s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 651s 7 414 414 185240536 246679946 0.269742 0.9692395 1.685273 651s Number of TCNs: 1111 651s Number of DHs: 414 651s int [1:1111] 6214 6215 6216 6217 6218 6219 6220 6221 6222 6223 ... 651s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 651s int [1:1111] 6214 6215 6216 6217 6218 6219 6220 6221 6222 6223 ... 651s Identify loci used to bootstrap DH means... 651s Heterozygous SNPs to resample for DH: 651s int [1:414] 6215 6216 6223 6224 6225 6230 6231 6234 6235 6236 ... 651s Identify loci used to bootstrap DH means...done 651s Identify loci used to bootstrap TCN means... 651s SNPs: 651s int [1:414] 6215 6216 6223 6224 6225 6230 6231 6234 6235 6236 ... 651s Non-polymorphic loci: 651s int [1:697] 6214 6217 6218 6219 6220 6221 6222 6226 6227 6228 ... 651s Heterozygous SNPs to resample for TCN: 651s int [1:414] 6215 6216 6223 6224 6225 6230 6231 6234 6235 6236 ... 651s Homozygous SNPs to resample for TCN: 651s int(0) 651s Non-polymorphic loci to resample for TCN: 651s int [1:697] 6214 6217 6218 6219 6220 6221 6222 6226 6227 6228 ... 651s Heterozygous SNPs with non-DH to resample for TCN: 651s int(0) 651s Loci to resample for TCN: 651s int [1:1111] 6214 6215 6216 6217 6218 6219 6220 6221 6222 6223 ... 651s Identify loci used to bootstrap TCN means...done 651s Number of (#hets, #homs, #nonSNPs): (414,0,697) 651s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 651s Number of bootstrap samples: 100 651s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 651s Segment #7 (chr 2, tcnId=3, dhId=1) of 7...done 651s Bootstrapped segment mean levels 651s num [1:7, 1:100, 1:4] 1.4 2.09 2.64 NA 1.39 ... 651s - attr(*, "dimnames")=List of 3 651s ..$ : NULL 651s ..$ : NULL 651s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 651s Calculating (C1,C2) mean levels from (TCN,DH) mean levels... 651s num [1:7, 1:100, 1:4] 1.4 2.09 2.64 NA 1.39 ... 651s - attr(*, "dimnames")=List of 3 651s ..$ : NULL 651s ..$ : NULL 651s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 651s Calculating (C1,C2) mean levels from (TCN,DH) mean levels...done 651s Calculating polar (alpha,radius,manhattan) for change points... 651s num [1:6, 1:100, 1:2] -0.448 -0.131 NA NA -0.477 ... 651s - attr(*, "dimnames")=List of 3 651s ..$ : NULL 651s ..$ : NULL 651s ..$ : chr [1:2] "c1" "c2" 651s Bootstrapped change points 651s num [1:6, 1:100, 1:5] -2.65 -1.87 NA NA -2.72 ... 651s - attr(*, "dimnames")=List of 3 651s ..$ : NULL 651s ..$ : NULL 651s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 651s Calculating polar (alpha,radius,manhattan) for change points...done 651s Bootstrapping (TCN,DH,C1,C2) segment mean levels...done 651s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data... 651s num [1:7, 1:4, 1:4] NA NA NA NA NA NA NA NA NA NA ... 651s - attr(*, "dimnames")=List of 3 651s ..$ : NULL 651s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 651s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 651s Field #1 ('tcn') of 4... 651s Segment #1 of 7... 651s Segment #1 of 7...done 651s Segment #2 of 7... 651s Segment #2 of 7...done 651s Segment #3 of 7... 651s Segment #3 of 7...done 651s Segment #4 of 7... 651s Segment #4 of 7...done 651s Segment #5 of 7... 651s Segment #5 of 7...done 651s Segment #6 of 7... 651s Segment #6 of 7...done 651s Segment #7 of 7... 651s Segment #7 of 7...done 651s Field #1 ('tcn') of 4...done 651s Field #2 ('dh') of 4... 651s Segment #1 of 7... 651s Segment #1 of 7...done 651s Segment #2 of 7... 651s Segment #2 of 7...done 651s Segment #3 of 7... 651s Segment #3 of 7...done 651s Segment #4 of 7... 651s Segment #4 of 7...done 651s Segment #5 of 7... 651s Segment #5 of 7...done 651s Segment #6 of 7... 651s Segment #6 of 7...done 651s Segment #7 of 7... 651s Segment #7 of 7...done 651s Field #2 ('dh') of 4...done 651s Field #3 ('c1') of 4... 651s Segment #1 of 7... 651s Segment #1 of 7...done 651s Segment #2 of 7... 651s Segment #2 of 7...done 651s Segment #3 of 7... 651s Segment #3 of 7...done 651s Segment #4 of 7... 651s Segment #4 of 7...done 651s Segment #5 of 7... 651s Segment #5 of 7...done 651s Segment #6 of 7... 651s Segment #6 of 7...done 651s Segment #7 of 7... 651s Segment #7 of 7...done 651s Field #3 ('c1') of 4...done 651s Field #4 ('c2') of 4... 651s Segment #1 of 7... 651s Segment #1 of 7...done 651s Segment #2 of 7... 651s Segment #2 of 7...done 651s Segment #3 of 7... 651s Segment #3 of 7...done 651s Segment #4 of 7... 651s Segment #4 of 7...done 651s Segment #5 of 7... 651s Segment #5 of 7...done 651s Segment #6 of 7... 651s Segment #6 of 7...done 651s Segment #7 of 7... 651s Segment #7 of 7...done 651s Field #4 ('c2') of 4...done 651s Bootstrap statistics 651s num [1:7, 1:4, 1:4] 1.38 2.07 2.63 NA 1.38 ... 651s - attr(*, "dimnames")=List of 3 651s ..$ : NULL 651s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 651s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 651s Statistical sanity checks (iff B >= 100)... 651s Available summaries: 2.5%, 5%, 95%, 97.5% 651s Available quantiles: 0.025, 0.05, 0.95, 0.975 651s num [1:7, 1:4, 1:4] 1.38 2.07 2.63 NA 1.38 ... 651s - attr(*, "dimnames")=List of 3 651s ..$ : NULL 651s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 651s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 651s Field #1 ('tcn') of 4... 651s Seg 1. mean=1.39161, range=[1.38025,1.40693], n=1880 651s Seg 2. mean=2.09245, range=[2.06856,2.1165], n=671 651s Seg 3. mean=2.65451, range=[2.62678,2.6834], n=1111 651s Seg 4. mean=NA, range=[NA,NA], n=NA 651s Seg 5. mean=1.39161, range=[1.37999,1.40474], n=1880 651s Seg 6. mean=2.09245, range=[2.06923,2.11747], n=671 651s Seg 7. mean=2.65451, range=[2.62867,2.68639], n=1111 651s Field #1 ('tcn') of 4...done 651s Field #2 ('dh') of 4... 651s Seg 1. mean=0.420632, range=[0.406983,0.437756], n=765 651s Seg 2. mean=0.176243, range=[0.141232,0.202975], n=272 651s Seg 3. mean=0.269742, range=[0.245337,0.292784], n=414 651s Seg 4. mean=NA, range=[NA,NA], n=NA 651s Seg 5. mean=0.420632, range=[0.406204,0.436189], n=765 651s Seg 6. mean=0.176243, range=[0.13696,0.212132], n=272 651s Seg 7. mean=0.269742, range=[0.230034,0.296763], n=414 651s Field #2 ('dh') of 4...done 651s Field #3 ('c1') of 4... 651s Seg 1. mean=0.403126, range=[0.391189,0.413437], n=765 651s Seg 2. mean=0.861836, range=[0.833296,0.900874], n=272 651s Seg 3. mean=0.969239, range=[0.937437,1.00659], n=414 651s Seg 4. mean=NA, range=[NA,NA], n=NA 651s Seg 5. mean=0.403126, range=[0.392112,0.414529], n=765 651s Seg 6. mean=0.861836, range=[0.823193,0.907577], n=272 651s Seg 7. mean=0.969239, range=[0.931951,1.01968], n=414 651s Field #3 ('c1') of 4...done 651s Field #4 ('c2') of 4... 651s Seg 1. mean=0.988482, range=[0.974501,1.00244], n=765 651s Seg 2. mean=1.23062, range=[1.18964,1.26157], n=272 651s Seg 3. mean=1.68527, range=[1.6481,1.72497], n=414 651s Seg 4. mean=NA, range=[NA,NA], n=NA 651s Seg 5. mean=0.988482, range=[0.9761,1.00076], n=765 651s Seg 6. mean=1.23062, range=[1.18936,1.26647], n=272 651s Seg 7. mean=1.68527, range=[1.63171,1.72526], n=414 651s Field #4 ('c2') of 4...done 651s Statistical sanity checks (iff B >= 100)...done 651s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data...done 651s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data... 651s num [1:6, 1:4, 1:5] NA NA NA NA NA NA NA NA NA NA ... 651s - attr(*, "dimnames")=List of 3 651s ..$ : NULL 651s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 651s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 651s Field #1 ('alpha') of 5... 651s Changepoint #1 of 6... 651s Changepoint #1 of 6...done 651s Changepoint #2 of 6... 651s Changepoint #2 of 6...done 651s Changepoint #3 of 6... 651s Changepoint #3 of 6...done 651s Changepoint #4 of 6... 651s Changepoint #4 of 6...done 651s Changepoint #5 of 6... 651s Changepoint #5 of 6...done 651s Changepoint #6 of 6... 651s Changepoint #6 of 6...done 651s Field #1 ('alpha') of 5...done 651s Field #2 ('radius') of 5... 651s Changepoint #1 of 6... 651s Changepoint #1 of 6...done 651s Changepoint #2 of 6... 651s Changepoint #2 of 6...done 651s Changepoint #3 of 6... 651s Changepoint #3 of 6...done 651s Changepoint #4 of 6... 651s Changepoint #4 of 6...done 651s Changepoint #5 of 6... 651s Changepoint #5 of 6...done 651s Changepoint #6 of 6... 651s Changepoint #6 of 6...done 651s Field #2 ('radius') of 5...done 651s Field #3 ('manhattan') of 5... 651s Changepoint #1 of 6... 651s Changepoint #1 of 6...done 651s Changepoint #2 of 6... 651s Changepoint #2 of 6...done 651s Changepoint #3 of 6... 651s Changepoint #3 of 6...done 651s Changepoint #4 of 6... 651s Changepoint #4 of 6...done 651s Changepoint #5 of 6... 651s Changepoint #5 of 6...done 651s Changepoint #6 of 6... 651s Changepoint #6 of 6...done 651s Field #3 ('manhattan') of 5...done 651s Field #4 ('d1') of 5... 651s Changepoint #1 of 6... 651s Changepoint #1 of 6...done 651s Changepoint #2 of 6... 651s Changepoint #2 of 6...done 651s Changepoint #3 of 6... 651s Changepoint #3 of 6...done 651s Changepoint #4 of 6... 651s Changepoint #4 of 6...done 651s Changepoint #5 of 6... 651s Changepoint #5 of 6...done 651s Changepoint #6 of 6... 651s Changepoint #6 of 6...done 651s Field #4 ('d1') of 5...done 651s Field #5 ('d2') of 5... 651s Changepoint #1 of 6... 651s Changepoint #1 of 6...done 651s Changepoint #2 of 6... 651s Changepoint #2 of 6...done 651s Changepoint #3 of 6... 651s Changepoint #3 of 6...done 651s Changepoint #4 of 6... 651s Changepoint #4 of 6...done 651s Changepoint #5 of 6... 651s Changepoint #5 of 6...done 651s Changepoint #6 of 6... 651s Changepoint #6 of 6...done 651s Field #5 ('d2') of 5...done 651s Bootstrap statistics 651s num [1:6, 1:4, 1:5] -2.76 -1.91 NA NA -2.76 ... 651s - attr(*, "dimnames")=List of 3 651s ..$ : NULL 651s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 651s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 651s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data...done 651s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint...done 651s > print(fit) 651s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 1 1 1 1 554484 143663981 1880 1.391608 765 651s 2 1 2 1 143663981 185240536 671 2.092452 272 651s 3 1 3 1 185240536 246679946 1111 2.654512 414 651s 4 NA NA NA NA NA NA NA NA 651s 5 2 1 1 554484 143663981 1880 1.391608 765 651s 6 2 2 1 143663981 185240536 671 2.092452 272 651s 7 2 3 1 185240536 246679946 1111 2.654512 414 651s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 651s 1 765 765 0.4206323 0.4031263 0.9884817 651s 2 272 272 0.1762428 0.8618360 1.2306156 651s 3 414 414 0.2697420 0.9692395 1.6852728 651s 4 NA NA NA NA NA 651s 5 765 765 0.4206323 0.4031263 0.9884817 651s 6 272 272 0.1762428 0.8618360 1.2306156 651s 7 414 414 0.2697420 0.9692395 1.6852728 651s > 651s > 651s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 651s > # Calling segments in allelic balance (AB) 651s > # NOTE: Ideally, this should be done on whole-genome data 651s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 651s > # Explicitly estimate the threshold in DH for calling AB 651s > # (which be done by default by the caller, if skipped here) 651s > deltaAB <- estimateDeltaAB(fit, flavor="qq(DH)", verbose=-10) 651s Estimating DH threshold for calling allelic imbalances... 651s flavor: qq(DH) 651s scale: 1 651s Estimating DH threshold for AB caller... 651s quantile #1: 0.05 651s Symmetric quantile #2: 0.9 651s Number of segments: 6 651s Weighted 5% quantile of DH: 0.199618 651s Number of segments with small DH: 2 651s Number of data points: 1342 651s Number of finite data points: 544 651s Estimate of (1-0.9):th and 50% quantiles: (0.0289919,0.176243) 651s Estimate of 0.9:th "symmetric" quantile: 0.323494 651s Estimating DH threshold for AB caller...done 651s Estimated delta: 0.323 651s Estimating DH threshold for calling allelic imbalances...done 651s > print(deltaAB) 651s [1] 0.3234938 651s > 651s > fit <- callAB(fit, delta=deltaAB, verbose=-10) 651s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 651s delta (offset adjusting for bias in DH): 0.323493772175137 651s alpha (CI quantile; significance level): 0.05 651s Calling segments... 651s Number of segments called allelic balance (AB): 4 (57.14%) of 7 651s Calling segments...done 651s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 651s > print(fit) 651s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 1 1 1 1 554484 143663981 1880 1.391608 765 651s 2 1 2 1 143663981 185240536 671 2.092452 272 651s 3 1 3 1 185240536 246679946 1111 2.654512 414 651s 4 NA NA NA NA NA NA NA NA 651s 5 2 1 1 554484 143663981 1880 1.391608 765 651s 6 2 2 1 143663981 185240536 671 2.092452 272 651s 7 2 3 1 185240536 246679946 1111 2.654512 414 651s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean abCall 651s 1 765 765 0.4206323 0.4031263 0.9884817 FALSE 651s 2 272 272 0.1762428 0.8618360 1.2306156 TRUE 651s 3 414 414 0.2697420 0.9692395 1.6852728 TRUE 651s 4 NA NA NA NA NA NA 651s 5 765 765 0.4206323 0.4031263 0.9884817 FALSE 651s 6 272 272 0.1762428 0.8618360 1.2306156 TRUE 651s 7 414 414 0.2697420 0.9692395 1.6852728 TRUE 651s > 651s > 651s > # Even if not explicitly specified, the estimated 651s > # threshold parameter is returned by the caller 651s > stopifnot(fit$params$deltaAB == deltaAB) 651s > 651s > 651s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 651s > # Calling segments in loss-of-heterozygosity (LOH) 651s > # NOTE: Ideally, this should be done on whole-genome data 651s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 651s > # Explicitly estimate the threshold in C1 for calling LOH 651s > # (which be done by default by the caller, if skipped here) 651s > deltaLOH <- estimateDeltaLOH(fit, flavor="minC1|nonAB", verbose=-10) 651s Estimating DH threshold for calling LOH... 651s flavor: minC1|nonAB 651s Estimating DH threshold for calling LOH as the midpoint between guessed C1=0 and C1=1... 651s Argument 'midpoint': 0.5 651s Number of segments: 6 651s Number of segments in allelic balance: 4 (66.7%) of 6 651s Number of segments not in allelic balance: 2 (33.3%) of 6 651s Number of segments in allelic balance and TCN <= 3.00: 4 (66.7%) of 6 651s C: 2.09, 2.65, 2.09, 2.65 651s Corrected C1 (=C/2): 1.05, 1.33, 1.05, 1.33 651s Number of DHs: 272, 414, 272, 414 651s Weights: 0.198, 0.302, 0.198, 0.302 651s Weighted median of (corrected) C1 in allelic balance: 1.274 651s Smallest C1 among segments not in allelic balance: 0.403 651s There are 2 segments with in total 765 heterozygous SNPs with this level. 651s There are 2 segments with in total 765 heterozygous SNPs with this level. 651s Midpoint between the two: 0.839 651s Estimating DH threshold for calling LOH as the midpoint between guessed C1=0 and C1=1...done 651s delta: 0.839 651s Estimating DH threshold for calling LOH...done 651s > print(deltaLOH) 651s [1] 0.838563 651s > 651s > fit <- callLOH(fit, delta=deltaLOH, verbose=-10) 651s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 651s delta (offset adjusting for bias in C1): 0.838562992888546 651s alpha (CI quantile; significance level): 0.05 651s Calling segments... 651s Number of segments called low C1 (LowC1, "LOH_C1"): 3 (42.86%) of 7 651s Calling segments...done 651s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 651s > print(fit) 651s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 651s 1 1 1 1 554484 143663981 1880 1.391608 765 651s 2 1 2 1 143663981 185240536 671 2.092452 272 651s 3 1 3 1 185240536 246679946 1111 2.654512 414 651s 4 NA NA NA NA NA NA NA NA 651s 5 2 1 1 554484 143663981 1880 1.391608 765 651s 6 2 2 1 143663981 185240536 671 2.092452 272 651s 7 2 3 1 185240536 246679946 1111 2.654512 414 651s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean abCall lohCall 651s 1 765 765 0.4206323 0.4031263 0.9884817 FALSE TRUE 651s 2 272 272 0.1762428 0.8618360 1.2306156 TRUE NA 651s 3 414 414 0.2697420 0.9692395 1.6852728 TRUE FALSE 651s 4 NA NA NA NA NA NA NA 651s 5 765 765 0.4206323 0.4031263 0.9884817 FALSE TRUE 651s 6 272 272 0.1762428 0.8618360 1.2306156 TRUE FALSE 651s 7 414 414 0.2697420 0.9692395 1.6852728 TRUE FALSE 651s > plotTracks(fit) 651s > 651s > # Even if not explicitly specified, the estimated 651s > # threshold parameter is returned by the caller 651s > stopifnot(fit$params$deltaLOH == deltaLOH) 651s > 651s > proc.time() 651s user system elapsed 651s 12.357 0.737 13.055 651s Test segmentByNonPairedPSCBS,medianDH passed 651s 0 651s Begin test segmentByPairedPSCBS,DH 651s + [ 0 != 0 ] 651s + echo Test segmentByNonPairedPSCBS,medianDH passed 651s + echo 0 651s + echo Begin test segmentByPairedPSCBS,DH 651s + exitcode=0 651s + R CMD BATCH segmentByPairedPSCBS,DH.R 667s + cat segmentByPairedPSCBS,DH.Rout 667s 667s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 667s Copyright (C) 2024 The R Foundation for Statistical Computing 667s Platform: aarch64-unknown-linux-gnu (64-bit) 667s 667s R is free software and comes with ABSOLUTELY NO WARRANTY. 667s You are welcome to redistribute it under certain conditions. 667s Type 'license()' or 'licence()' for distribution details. 667s 667s R is a collaborative project with many contributors. 667s Type 'contributors()' for more information and 667s 'citation()' on how to cite R or R packages in publications. 667s 667s Type 'demo()' for some demos, 'help()' for on-line help, or 667s 'help.start()' for an HTML browser interface to help. 667s Type 'q()' to quit R. 667s 667s [Previously saved workspace restored] 667s 667s > library("PSCBS") 667s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 667s 667s Attaching package: 'PSCBS' 667s 667s The following objects are masked from 'package:base': 667s 667s append, load 667s 667s > 667s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 667s > # Load SNP microarray data 667s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 667s > data <- PSCBS::exampleData("paired.chr01") 667s > str(data) 667s 'data.frame': 73346 obs. of 6 variables: 667s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 667s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 667s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 667s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 667s $ CN : num 2.36 2.13 2.59 1.93 1.71 ... 667s $ betaN : num 0.827 0.875 0.887 0.884 0.103 ... 667s > 667s > # Drop single-locus outliers 667s > dataS <- dropSegmentationOutliers(data) 667s > 667s > # Run light-weight tests 667s > # Use only every 5th data point 667s > dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 667s > # Number of segments (for assertion) 667s > nSegs <- 3L 667s > # Number of bootstrap samples (see below) 667s > B <- 100L 667s > 667s > str(dataS) 667s 'data.frame': 14670 obs. of 6 variables: 667s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 667s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 667s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 667s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 667s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 667s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 667s > R.oo::attachLocally(dataS) 667s > 667s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 667s > # Calculate DH 667s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 667s > muN <- aroma.light::callNaiveGenotypes(betaN, censorAt=c(0,1)) 667s > # SNPs are identifies as those loci that have non-missing 'betaT' & 'muN' 667s > isSnp <- (!is.na(betaT) & !is.na(muN)) 667s > isHet <- isSnp & (muN == 1/2) 667s > rho <- rep(NA_real_, length=length(muN)) 667s > rho[isHet] <- 2*abs(betaT[isHet]-1/2) 667s > 667s > 667s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 667s > # Paired PSCBS segmentation using TCN and DH only 667s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 667s > fit <- segmentByPairedPSCBS(CT, rho=rho, 667s + chromosome=chromosome, x=x, 667s + seed=0xBEEF, verbose=-10) 667s Segmenting paired tumor-normal signals using Paired PSCBS... 667s Setup up data... 667s 'data.frame': 14670 obs. of 4 variables: 667s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 667s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 667s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 667s $ rho : num NA 0.662 NA NA NA ... 667s Setup up data...done 667s Dropping loci for which TCNs are missing... 667s Number of loci dropped: 12 667s Dropping loci for which TCNs are missing...done 667s Ordering data along genome... 667s 'data.frame': 14658 obs. of 4 variables: 667s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 667s $ x : num 554484 730720 782343 878522 916294 ... 667s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 667s $ rho : num NA NA NA NA NA ... 667s Ordering data along genome...done 667s Keeping only current chromosome for 'knownSegments'... 667s Chromosome: 1 667s Known segments for this chromosome: 667s [1] chromosome start end 667s <0 rows> (or 0-length row.names) 667s Keeping only current chromosome for 'knownSegments'...done 667s alphaTCN: 0.009 667s alphaDH: 0.001 667s Number of loci: 14658 667s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 667s Produced 2 seeds from this stream for future usage 667s Identification of change points by total copy numbers... 667s Segmenting by CBS... 667s Chromosome: 1 667s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 667s Segmenting by CBS...done 667s List of 4 667s $ data :'data.frame': 14658 obs. of 4 variables: 667s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 667s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 667s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 667s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 667s $ output :'data.frame': 3 obs. of 6 variables: 667s ..$ sampleName: chr [1:3] NA NA NA 667s ..$ chromosome: int [1:3] 1 1 1 667s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 667s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 667s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 667s ..$ mean : num [1:3] 1.39 2.07 2.63 667s $ segRows:'data.frame': 3 obs. of 2 variables: 667s ..$ startRow: int [1:3] 1 7600 10268 667s ..$ endRow : int [1:3] 7599 10267 14658 667s $ params :List of 5 667s ..$ alpha : num 0.009 667s ..$ undo : num 0 667s ..$ joinSegments : logi TRUE 667s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 667s .. ..$ chromosome: int 1 667s .. ..$ start : num -Inf 667s .. ..$ end : num Inf 667s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 667s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 667s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 1.8 0 1.8 0 0 667s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 667s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 667s - attr(*, "randomSeed")= int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 667s Identification of change points by total copy numbers...done 667s Restructure TCN segmentation results... 667s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 667s 1 1 554484 143926517 7599 1.3859 667s 2 1 143926517 185449813 2668 2.0704 667s 3 1 185449813 247137334 4391 2.6341 667s Number of TCN segments: 3 667s Restructure TCN segmentation results...done 667s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 667s Number of TCN loci in segment: 7599 667s Locus data for TCN segment: 667s 'data.frame': 7599 obs. of 5 variables: 667s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 667s $ x : num 554484 730720 782343 878522 916294 ... 667s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 667s $ rho : num NA NA NA NA NA ... 667s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 667s Number of loci: 7599 667s Number of SNPs: 2111 (27.78%) 667s Number of heterozygous SNPs: 2111 (100.00%) 667s Chromosome: 1 667s Segmenting DH signals... 667s Segmenting by CBS... 667s Chromosome: 1 667s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 667s Segmenting by CBS...done 667s List of 4 667s $ data :'data.frame': 7599 obs. of 4 variables: 667s ..$ chromosome: int [1:7599] 1 1 1 1 1 1 1 1 1 1 ... 667s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 667s ..$ y : num [1:7599] NA NA NA NA NA ... 667s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 667s $ output :'data.frame': 1 obs. of 6 variables: 667s ..$ sampleName: chr NA 667s ..$ chromosome: int 1 667s ..$ start : num 554484 667s ..$ end : num 1.44e+08 667s ..$ nbrOfLoci : int 2111 667s ..$ mean : num 0.524 667s $ segRows:'data.frame': 1 obs. of 2 variables: 667s ..$ startRow: int 10 667s ..$ endRow : int 7594 667s $ params :List of 5 667s ..$ alpha : num 0.001 667s ..$ undo : num 0 667s ..$ joinSegments : logi TRUE 667s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 667s .. ..$ chromosome: int 1 667s .. ..$ start : num 554484 667s .. ..$ end : num 1.44e+08 667s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 667s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 667s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.077 0 0.078 0 0 667s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 667s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 667s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 667s DH segmentation (locally-indexed) rows: 667s startRow endRow 667s 1 10 7594 667s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 667s DH segmentation rows: 667s startRow endRow 667s 1 10 7594 667s Segmenting DH signals...done 667s DH segmentation table: 667s dhStart dhEnd dhNbrOfLoci dhMean 667s 1 554484 143926517 2111 0.5237 667s startRow endRow 667s 1 10 7594 667s Rows: 667s [1] 1 667s TCN segmentation rows: 667s startRow endRow 667s 1 1 7599 667s TCN and DH segmentation rows: 667s startRow endRow 667s 1 1 7599 667s startRow endRow 667s 1 10 7594 667s NULL 667s TCN segmentation (expanded) rows: 667s startRow endRow 667s 1 1 7599 667s TCN and DH segmentation rows: 667s startRow endRow 667s 1 1 7599 667s 2 7600 10267 667s 3 10268 14658 667s startRow endRow 667s 1 10 7594 667s startRow endRow 667s 1 1 7599 667s Total CN segmentation table (expanded): 667s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 667s 1 1 554484 143926517 7599 1.3859 2111 2111 667s (TCN,DH) segmentation for one total CN segment: 667s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 667s 1 1 1 1 554484 143926517 7599 1.3859 2111 667s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 667s 1 2111 554484 143926517 2111 0.5237 667s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 667s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 667s Number of TCN loci in segment: 2668 667s Locus data for TCN segment: 667s 'data.frame': 2668 obs. of 5 variables: 667s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 667s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 667s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 667s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 667s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 667s Number of loci: 2668 667s Number of SNPs: 774 (29.01%) 667s Number of heterozygous SNPs: 774 (100.00%) 667s Chromosome: 1 667s Segmenting DH signals... 667s Segmenting by CBS... 667s Chromosome: 1 667s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 667s Segmenting by CBS...done 667s List of 4 667s $ data :'data.frame': 2668 obs. of 4 variables: 667s ..$ chromosome: int [1:2668] 1 1 1 1 1 1 1 1 1 1 ... 667s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 667s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 667s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 667s $ output :'data.frame': 1 obs. of 6 variables: 667s ..$ sampleName: chr NA 667s ..$ chromosome: int 1 667s ..$ start : num 1.44e+08 667s ..$ end : num 1.85e+08 667s ..$ nbrOfLoci : int 774 667s ..$ mean : num 0.154 667s $ segRows:'data.frame': 1 obs. of 2 variables: 667s ..$ startRow: int 15 667s ..$ endRow : int 2664 667s $ params :List of 5 667s ..$ alpha : num 0.001 667s ..$ undo : num 0 667s ..$ joinSegments : logi TRUE 667s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 667s .. ..$ chromosome: int 1 667s .. ..$ start : num 1.44e+08 667s .. ..$ end : num 1.85e+08 667s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 667s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 667s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.03 0 0.031 0 0 667s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 667s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 667s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 667s DH segmentation (locally-indexed) rows: 667s startRow endRow 667s 1 15 2664 667s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 667s DH segmentation rows: 667s startRow endRow 667s 1 7614 10263 667s Segmenting DH signals...done 667s DH segmentation table: 667s dhStart dhEnd dhNbrOfLoci dhMean 667s 1 143926517 185449813 774 0.1542 667s startRow endRow 667s 1 7614 10263 667s Rows: 667s [1] 2 667s TCN segmentation rows: 667s startRow endRow 667s 2 7600 10267 667s TCN and DH segmentation rows: 667s startRow endRow 667s 2 7600 10267 667s startRow endRow 667s 1 7614 10263 667s startRow endRow 667s 1 1 7599 667s TCN segmentation (expanded) rows: 667s startRow endRow 667s 1 1 7599 667s 2 7600 10267 667s TCN and DH segmentation rows: 667s startRow endRow 667s 1 1 7599 667s 2 7600 10267 667s 3 10268 14658 667s startRow endRow 667s 1 10 7594 667s 2 7614 10263 667s startRow endRow 667s 1 1 7599 667s 2 7600 10267 667s Total CN segmentation table (expanded): 667s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 667s 2 1 143926517 185449813 2668 2.0704 774 774 667s (TCN,DH) segmentation for one total CN segment: 667s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 667s 2 2 1 1 143926517 185449813 2668 2.0704 774 667s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 667s 2 774 143926517 185449813 774 0.1542 667s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 667s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 667s Number of TCN loci in segment: 4391 667s Locus data for TCN segment: 667s 'data.frame': 4391 obs. of 5 variables: 667s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 667s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 667s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 667s $ rho : num NA 0.0308 NA 0.2533 NA ... 667s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 667s Number of loci: 4391 667s Number of SNPs: 1311 (29.86%) 667s Number of heterozygous SNPs: 1311 (100.00%) 667s Chromosome: 1 667s Segmenting DH signals... 667s Segmenting by CBS... 667s Chromosome: 1 667s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 667s Segmenting by CBS...done 667s List of 4 667s $ data :'data.frame': 4391 obs. of 4 variables: 667s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 667s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 667s ..$ y : num [1:4391] NA 0.0308 NA 0.2533 NA ... 667s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 667s $ output :'data.frame': 1 obs. of 6 variables: 667s ..$ sampleName: chr NA 667s ..$ chromosome: int 1 667s ..$ start : num 1.85e+08 667s ..$ end : num 2.47e+08 667s ..$ nbrOfLoci : int 1311 667s ..$ mean : num 0.251 667s $ segRows:'data.frame': 1 obs. of 2 variables: 667s ..$ startRow: int 2 667s ..$ endRow : int 4388 667s $ params :List of 5 667s ..$ alpha : num 0.001 667s ..$ undo : num 0 667s ..$ joinSegments : logi TRUE 667s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 667s .. ..$ chromosome: int 1 667s .. ..$ start : num 1.85e+08 667s .. ..$ end : num 2.47e+08 667s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 667s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 667s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.079 0 0.078 0 0 667s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 667s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 667s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 667s DH segmentation (locally-indexed) rows: 667s startRow endRow 667s 1 2 4388 667s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 667s DH segmentation rows: 667s startRow endRow 667s 1 10269 14655 667s Segmenting DH signals...done 667s DH segmentation table: 667s dhStart dhEnd dhNbrOfLoci dhMean 667s 1 185449813 247137334 1311 0.2512 667s startRow endRow 667s 1 10269 14655 667s Rows: 667s [1] 3 667s TCN segmentation rows: 667s startRow endRow 667s 3 10268 14658 667s TCN and DH segmentation rows: 667s startRow endRow 667s 3 10268 14658 667s startRow endRow 667s 1 10269 14655 667s startRow endRow 667s 1 1 7599 667s 2 7600 10267 667s TCN segmentation (expanded) rows: 667s startRow endRow 667s 1 1 7599 667s 2 7600 10267 667s 3 10268 14658 667s TCN and DH segmentation rows: 667s startRow endRow 667s 1 1 7599 667s 2 7600 10267 667s 3 10268 14658 667s startRow endRow 667s 1 10 7594 667s 2 7614 10263 667s 3 10269 14655 667s startRow endRow 667s 1 1 7599 667s 2 7600 10267 667s 3 10268 14658 667s Total CN segmentation table (expanded): 667s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 667s 3 1 185449813 247137334 4391 2.6341 1311 1311 667s (TCN,DH) segmentation for one total CN segment: 667s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 667s 3 3 1 1 185449813 247137334 4391 2.6341 1311 667s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 667s 3 1311 185449813 247137334 1311 0.2512 667s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 667s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 667s 1 1 1 1 554484 143926517 7599 1.3859 2111 667s 2 1 2 1 143926517 185449813 2668 2.0704 774 667s 3 1 3 1 185449813 247137334 4391 2.6341 1311 667s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 667s 1 2111 554484 143926517 2111 0.5237 667s 2 774 143926517 185449813 774 0.1542 667s 3 1311 185449813 247137334 1311 0.2512 667s Calculating (C1,C2) per segment... 667s Calculating (C1,C2) per segment...done 667s Number of segments: 3 667s Segmenting paired tumor-normal signals using Paired PSCBS...done 667s Post-segmenting TCNs... 667s Number of segments: 3 667s Number of chromosomes: 1 667s [1] 1 667s Chromosome 1 ('chr01') of 1... 667s Rows: 667s [1] 1 2 3 667s Number of segments: 3 667s TCN segment #1 ('1') of 3... 667s Nothing todo. Only one DH segmentation. Skipping. 667s TCN segment #1 ('1') of 3...done 667s TCN segment #2 ('2') of 3... 667s Nothing todo. Only one DH segmentation. Skipping. 667s TCN segment #2 ('2') of 3...done 667s TCN segment #3 ('3') of 3... 667s Nothing todo. Only one DH segmentation. Skipping. 667s TCN segment #3 ('3') of 3...done 667s Chromosome 1 ('chr01') of 1...done 667s Update (C1,C2) per segment... 667s Update (C1,C2) per segment...done 667s Post-segmenting TCNs...done 667s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 667s 1 1 1 1 554484 143926517 7599 1.3859 2111 667s 2 1 2 1 143926517 185449813 2668 2.0704 774 667s 3 1 3 1 185449813 247137334 4391 2.6341 1311 667s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 667s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 667s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 667s 3 1311 185449813 247137334 1311 0.2512 0.9862070 1.647893 667s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 667s 1 1 1 1 554484 143926517 7599 1.3859 2111 667s 2 1 2 1 143926517 185449813 2668 2.0704 774 667s 3 1 3 1 185449813 247137334 4391 2.6341 1311 667s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 667s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 667s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 667s 3 1311 185449813 247137334 1311 0.2512 0.9862070 1.647893 667s > print(fit) 667s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 667s 1 1 1 1 554484 143926517 7599 1.3859 2111 667s 2 1 2 1 143926517 185449813 2668 2.0704 774 667s 3 1 3 1 185449813 247137334 4391 2.6341 1311 667s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 667s 1 2111 2111 0.5237 0.3300521 1.055848 667s 2 774 774 0.1542 0.8755722 1.194828 667s 3 1311 1311 0.2512 0.9862070 1.647893 667s > 667s > # Plot results 667s > plotTracks(fit) 667s > 667s > 667s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 667s > # Bootstrap segment level estimates 667s > # (used by the AB caller, which, if skipped here, 667s > # will do it automatically) 667s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 667s > fit <- bootstrapTCNandDHByRegion(fit, B=B, verbose=-10) 667s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint... 667s Already done? 667s tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% dh_97.5% 667s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 667s c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% c2_97.5% 667s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 667s Bootstrapping (TCN,DH,C1,C2) segment mean levels... 667s Identifying heterozygous & homozygous SNPs and non-polymorphic loci... 667s Number of loci: 14658 667s Number of SNPs: 4196 667s Number of non-SNPs: 10462 667s Identifying heterozygous & homozygous SNPs and non-polymorphic loci...done 667s num [1:3, 1:100, 1:4] NA NA NA NA NA NA NA NA NA NA ... 667s - attr(*, "dimnames")=List of 3 667s ..$ : NULL 667s ..$ : NULL 667s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 667s Segment #1 (chr 1, tcnId=1, dhId=1) of 3... 667s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 667s 1 1 1 1 554484 143926517 7599 1.3859 2111 667s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 667s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 667s Number of TCNs: 7599 667s Number of DHs: 2111 667s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 667s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 667s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 667s Identify loci used to bootstrap DH means... 667s Heterozygous SNPs to resample for DH: 667s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 667s Identify loci used to bootstrap DH means...done 667s Identify loci used to bootstrap TCN means... 667s SNPs: 667s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 667s Non-polymorphic loci: 667s int [1:5488] 1 2 3 4 5 6 7 8 9 11 ... 667s Heterozygous SNPs to resample for TCN: 667s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 667s Homozygous SNPs to resample for TCN: 667s int(0) 667s Non-polymorphic loci to resample for TCN: 667s int [1:5488] 1 2 3 4 5 6 7 8 9 11 ... 667s Heterozygous SNPs with non-DH to resample for TCN: 667s int(0) 667s Loci to resample for TCN: 667s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 667s Identify loci used to bootstrap TCN means...done 667s Number of (#hets, #homs, #nonSNPs): (2111,0,5488) 667s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 667s Number of bootstrap samples: 100 667s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 667s Segment #1 (chr 1, tcnId=1, dhId=1) of 3...done 667s Segment #2 (chr 1, tcnId=2, dhId=1) of 3... 667s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 667s 2 1 2 1 143926517 185449813 2668 2.0704 774 667s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 667s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 667s Number of TCNs: 2668 667s Number of DHs: 774 667s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 667s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 667s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 667s Identify loci used to bootstrap DH means... 667s Heterozygous SNPs to resample for DH: 667s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 667s Identify loci used to bootstrap DH means...done 667s Identify loci used to bootstrap TCN means... 667s SNPs: 667s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 667s Non-polymorphic loci: 667s int [1:1894] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 667s Heterozygous SNPs to resample for TCN: 667s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 667s Homozygous SNPs to resample for TCN: 667s int(0) 667s Non-polymorphic loci to resample for TCN: 667s int [1:1894] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 667s Heterozygous SNPs with non-DH to resample for TCN: 667s int(0) 667s Loci to resample for TCN: 667s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 667s Identify loci used to bootstrap TCN means...done 667s Number of (#hets, #homs, #nonSNPs): (774,0,1894) 667s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 667s Number of bootstrap samples: 100 667s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 667s Segment #2 (chr 1, tcnId=2, dhId=1) of 3...done 667s Segment #3 (chr 1, tcnId=3, dhId=1) of 3... 667s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 667s 3 1 3 1 185449813 247137334 4391 2.6341 1311 667s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 667s 3 1311 185449813 247137334 1311 0.2512 0.986207 1.647893 667s Number of TCNs: 4391 667s Number of DHs: 1311 667s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 667s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 667s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 667s Identify loci used to bootstrap DH means... 667s Heterozygous SNPs to resample for DH: 667s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 667s Identify loci used to bootstrap DH means...done 667s Identify loci used to bootstrap TCN means... 667s SNPs: 667s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 667s Non-polymorphic loci: 667s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 667s Heterozygous SNPs to resample for TCN: 667s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 667s Homozygous SNPs to resample for TCN: 667s int(0) 667s Non-polymorphic loci to resample for TCN: 667s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 667s Heterozygous SNPs with non-DH to resample for TCN: 667s int(0) 667s Loci to resample for TCN: 667s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 667s Identify loci used to bootstrap TCN means...done 667s Number of (#hets, #homs, #nonSNPs): (1311,0,3080) 667s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 667s Number of bootstrap samples: 100 667s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 667s Segment #3 (chr 1, tcnId=3, dhId=1) of 3...done 667s Bootstrapped segment mean levels 667s num [1:3, 1:100, 1:4] 1.38 2.08 2.63 1.38 2.07 ... 667s - attr(*, "dimnames")=List of 3 667s ..$ : NULL 667s ..$ : NULL 667s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 667s Calculating (C1,C2) mean levels from (TCN,DH) mean levels... 667s num [1:3, 1:100, 1:4] 1.38 2.08 2.63 1.38 2.07 ... 667s - attr(*, "dimnames")=List of 3 667s ..$ : NULL 667s ..$ : NULL 667s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 667s Calculating (C1,C2) mean levels from (TCN,DH) mean levels...done 667s Calculating polar (alpha,radius,manhattan) for change points... 667s num [1:2, 1:100, 1:2] -0.5588 -0.0962 -0.5365 -0.1285 -0.5378 ... 667s - attr(*, "dimnames")=List of 3 667s ..$ : NULL 667s ..$ : NULL 667s ..$ : chr [1:2] "c1" "c2" 667s Bootstrapped change points 667s num [1:2, 1:100, 1:5] -2.89 -1.78 -2.87 -1.86 -2.88 ... 667s - attr(*, "dimnames")=List of 3 667s ..$ : NULL 667s ..$ : NULL 667s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 667s Calculating polar (alpha,radius,manhattan) for change points...done 667s Bootstrapping (TCN,DH,C1,C2) segment mean levels...done 667s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data... 667s num [1:3, 1:4, 1:4] NA NA NA NA NA NA NA NA NA NA ... 667s - attr(*, "dimnames")=List of 3 667s ..$ : NULL 667s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 667s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 667s Field #1 ('tcn') of 4... 667s Segment #1 of 3... 667s Segment #1 of 3...done 667s Segment #2 of 3... 667s Segment #2 of 3...done 667s Segment #3 of 3... 667s Segment #3 of 3...done 667s Field #1 ('tcn') of 4...done 667s Field #2 ('dh') of 4... 667s Segment #1 of 3... 667s Segment #1 of 3...done 667s Segment #2 of 3... 667s Segment #2 of 3...done 667s Segment #3 of 3... 667s Segment #3 of 3...done 667s Field #2 ('dh') of 4...done 667s Field #3 ('c1') of 4... 667s Segment #1 of 3... 667s Segment #1 of 3...done 667s Segment #2 of 3... 667s Segment #2 of 3...done 667s Segment #3 of 3... 667s Segment #3 of 3...done 667s Field #3 ('c1') of 4...done 667s Field #4 ('c2') of 4... 667s Segment #1 of 3... 667s Segment #1 of 3...done 667s Segment #2 of 3... 667s Segment #2 of 3...done 667s Segment #3 of 3... 667s Segment #3 of 3...done 667s Field #4 ('c2') of 4...done 667s Bootstrap statistics 667s num [1:3, 1:4, 1:4] 1.38 2.06 2.62 1.38 2.06 ... 667s - attr(*, "dimnames")=List of 3 667s ..$ : NULL 667s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 667s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 667s Statistical sanity checks (iff B >= 100)... 667s Available summaries: 2.5%, 5%, 95%, 97.5% 667s Available quantiles: 0.025, 0.05, 0.95, 0.975 667s num [1:3, 1:4, 1:4] 1.38 2.06 2.62 1.38 2.06 ... 667s - attr(*, "dimnames")=List of 3 667s ..$ : NULL 667s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 667s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 667s Field #1 ('tcn') of 4... 667s Seg 1. mean=1.3859, range=[1.38092,1.3949], n=7599 667s Seg 2. mean=2.0704, range=[2.05747,2.08326], n=2668 667s Seg 3. mean=2.6341, range=[2.62068,2.64694], n=4391 667s Field #1 ('tcn') of 4...done 667s Field #2 ('dh') of 4... 667s Seg 1. mean=0.5237, range=[0.51753,0.532002], n=2111 667s Seg 2. mean=0.1542, range=[0.144468,0.16453], n=774 667s Seg 3. mean=0.2512, range=[0.242575,0.258832], n=1311 667s Field #2 ('dh') of 4...done 667s Field #3 ('c1') of 4... 667s Seg 1. mean=0.330052, range=[0.323996,0.336038], n=2111 667s Seg 2. mean=0.875572, range=[0.86318,0.887699], n=774 667s Seg 3. mean=0.986207, range=[0.975123,0.998982], n=1311 667s Field #3 ('c1') of 4...done 667s Field #4 ('c2') of 4... 667s Seg 1. mean=1.05585, range=[1.05006,1.06231], n=2111 667s Seg 2. mean=1.19483, range=[1.18417,1.2081], n=774 667s Seg 3. mean=1.64789, range=[1.63403,1.66098], n=1311 667s Field #4 ('c2') of 4...done 667s Statistical sanity checks (iff B >= 100)...done 667s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data...done 667s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data... 667s num [1:2, 1:4, 1:5] NA NA NA NA NA NA NA NA NA NA ... 667s - attr(*, "dimnames")=List of 3 667s ..$ : NULL 667s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 667s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 667s Field #1 ('alpha') of 5... 667s Changepoint #1 of 2... 667s Changepoint #1 of 2...done 667s Changepoint #2 of 2... 667s Changepoint #2 of 2...done 667s Field #1 ('alpha') of 5...done 667s Field #2 ('radius') of 5... 667s Changepoint #1 of 2... 667s Changepoint #1 of 2...done 667s Changepoint #2 of 2... 667s Changepoint #2 of 2...done 667s Field #2 ('radius') of 5...done 667s Field #3 ('manhattan') of 5... 667s Changepoint #1 of 2... 667s Changepoint #1 of 2...done 667s Changepoint #2 of 2... 667s Changepoint #2 of 2...done 667s Field #3 ('manhattan') of 5...done 667s Field #4 ('d1') of 5... 667s Changepoint #1 of 2... 667s Changepoint #1 of 2...done 667s Changepoint #2 of 2... 667s Changepoint #2 of 2...done 667s Field #4 ('d1') of 5...done 667s Field #5 ('d2') of 5... 667s Changepoint #1 of 2... 667s Changepoint #1 of 2...done 667s Changepoint #2 of 2... 667s Changepoint #2 of 2...done 667s Field #5 ('d2') of 5...done 667s Bootstrap statistics 667s num [1:2, 1:4, 1:5] -2.92 -1.86 -2.91 -1.85 -2.87 ... 667s - attr(*, "dimnames")=List of 3 667s ..$ : NULL 667s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 667s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 667s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data...done 667s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint...done 667s > print(fit) 667s chromosome tcnId dhId start end tcnNbrOfLoci tcnMe+ [ 0 != 0 ] 667s + echo Test segmentByPairedPSCBS,DH passed 667s + echo 0 667s + echo Begin test segmentByPairedPSCBS,calls 667s + exitcode=0 667s + R CMD BATCH segmentByPairedPSCBS,calls.R 667s an tcnNbrOfSNPs 667s 1 1 1 1 554484 143926517 7599 1.3859 2111 667s 2 1 2 1 143926517 185449813 2668 2.0704 774 667s 3 1 3 1 185449813 247137334 4391 2.6341 1311 667s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 667s 1 2111 2111 0.5237 0.3300521 1.055848 667s 2 774 774 0.1542 0.8755722 1.194828 667s 3 1311 1311 0.2512 0.9862070 1.647893 667s > plotTracks(fit) 667s > 667s > 667s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 667s > # Calling segments in allelic balance (AB) and 667s > # in loss-of-heterozygosity (LOH) 667s > # NOTE: Ideally, this should be done on whole-genome data 667s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 667s > fit <- callAB(fit, verbose=-10) 667s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 667s delta (offset adjusting for bias in DH): 0.3466649145302 667s alpha (CI quantile; significance level): 0.05 667s Calling segments... 667s Number of segments called allelic balance (AB): 2 (66.67%) of 3 667s Calling segments...done 667s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 667s > fit <- callLOH(fit, verbose=-10) 667s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 667s delta (offset adjusting for bias in C1): 0.771236438183453 667s alpha (CI quantile; significance level): 0.05 667s Calling segments... 667s Number of segments called low C1 (LowC1, "LOH_C1"): 1 (33.33%) of 3 667s Calling segments...done 667s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 667s > print(fit) 667s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 667s 1 1 1 1 554484 143926517 7599 1.3859 2111 667s 2 1 2 1 143926517 185449813 2668 2.0704 774 667s 3 1 3 1 185449813 247137334 4391 2.6341 1311 667s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean abCall lohCall 667s 1 2111 2111 0.5237 0.3300521 1.055848 FALSE TRUE 667s 2 774 774 0.1542 0.8755722 1.194828 TRUE FALSE 667s 3 1311 1311 0.2512 0.9862070 1.647893 TRUE FALSE 667s > plotTracks(fit) 667s > 667s > proc.time() 667s user system elapsed 667s 12.978 0.799 13.733 667s Test segmentByPairedPSCBS,DH passed 667s 0 667s Begin test segmentByPairedPSCBS,calls 689s + 689s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 689s Copyright (C) 2024 The R Foundation for Statistical Computing 689s Platform: aarch64-unknown-linux-gnu (64-bit) 689s 689s R is free software and comes with ABSOLUTELY NO WARRANTY. 689s You are welcome to redistribute it under certain conditions. 689s Type 'license()' or 'licence()' for distribution details. 689s 689s R is a collaborative project with many contributors. 689s Type 'contributors()' for more information and 689s 'citation()' on how to cite R or R packages in publications. 689s 689s Type 'demo()' for some demos, 'help()' for on-line help, or 689s 'help.start()' for an HTML browser interface to help. 689s Type 'q()' to quit R. 689s 689s [Previously saved workspace restored] 689s 689s > library("PSCBS") 689s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 689s 689s Attaching package: 'PSCBS' 689s 689s The following objects are masked from 'package:base': 689s 689s append, load 689s 689s > 689s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 689s > # Load SNP microarray data 689s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 689s > data <- PSCBS::exampleData("paired.chr01") 689s > str(data) 689s 'data.frame': 73346 obs. of 6 variables: 689s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 689s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 689s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 689s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 689s $ CN : num 2.36 2.13 2.59 1.93 1.71 ... 689s $ betaN : num 0.827 0.875 0.887 0.884 0.103 ... 689s > 689s > 689s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 689s > # Paired PSCBS segmentation 689s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 689s > # Drop single-locus outliers 689s > dataS <- dropSegmentationOutliers(data) 689s > 689s > # Find centromere 689s > gaps <- findLargeGaps(dataS, minLength=2e6) 689s > knownSegments <- gapsToSegments(gaps) 689s > 689s > 689s > # Run light-weight tests by default 689s > if (Sys.getenv("_R_CHECK_FULL_") == "") { 689s + # Use only every 5th data point 689s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 689s + # Number of segments (for assertion) 689s + nSegs <- 4L 689s + # Number of bootstrap samples (see below) 689s + B <- 100L 689s + } else { 689s + # Full tests 689s + nSegs <- 11L 689s + B <- 1000L 689s + } 689s > 689s > str(dataS) 689s 'data.frame': 14670 obs. of 6 variables: 689s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 689s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 689s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 689s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 689s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 689s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 689s > 689s > # Paired PSCBS segmentation 689s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 689s + seed=0xBEEF, verbose=-10) 689s Segmenting paired tumor-normal signals using Paired PSCBS... 689s Calling genotypes from normal allele B fractions... 689s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 689s Called genotypes: 689s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 689s - attr(*, "modelFit")=List of 1 689s ..$ :List of 7 689s .. ..$ flavor : chr "density" 689s .. ..$ cn : int 2 689s .. ..$ nbrOfGenotypeGroups: int 3 689s .. ..$ tau : num [1:2] 0.315 0.677 689s .. ..$ n : int 14640 689s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 689s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 689s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 689s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 689s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 689s .. .. ..$ type : chr [1:2] "valley" "valley" 689s .. .. ..$ x : num [1:2] 0.315 0.677 689s .. .. ..$ density: num [1:2] 0.522 0.552 689s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 689s muN 689s 0 0.5 1 689s 5221 4198 5251 689s Calling genotypes from normal allele B fractions...done 689s Normalizing betaT using betaN (TumorBoost)... 689s Normalized BAFs: 689s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 689s - attr(*, "modelFit")=List of 5 689s ..$ method : chr "normalizeTumorBoost" 689s ..$ flavor : chr "v4" 689s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 689s .. ..- attr(*, "modelFit")=List of 1 689s .. .. ..$ :List of 7 689s .. .. .. ..$ flavor : chr "density" 689s .. .. .. ..$ cn : int 2 689s .. .. .. ..$ nbrOfGenotypeGroups: int 3 689s .. .. .. ..$ tau : num [1:2] 0.315 0.677 689s .. .. .. ..$ n : int 14640 689s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 689s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 689s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 689s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 689s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 689s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 689s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 689s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 689s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 689s ..$ preserveScale: logi FALSE 689s ..$ scaleFactor : num NA 689s Normalizing betaT using betaN (TumorBoost)...done 689s Setup up data... 689s 'data.frame': 14670 obs. of 7 variables: 689s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 689s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 689s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 689s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 689s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 689s ..- attr(*, "modelFit")=List of 5 689s .. ..$ method : chr "normalizeTumorBoost" 689s .. ..$ flavor : chr "v4" 689s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 689s .. .. ..- attr(*, "modelFit")=List of 1 689s .. .. .. ..$ :List of 7 689s .. .. .. .. ..$ flavor : chr "density" 689s .. .. .. .. ..$ cn : int 2 689s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 689s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 689s .. .. .. .. ..$ n : int 14640 689s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 689s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 689s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 689s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 689s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 689s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 689s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 689s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 689s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 689s .. ..$ preserveScale: logi FALSE 689s .. ..$ scaleFactor : num NA 689s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 689s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 689s ..- attr(*, "modelFit")=List of 1 689s .. ..$ :List of 7 689s .. .. ..$ flavor : chr "density" 689s .. .. ..$ cn : int 2 689s .. .. ..$ nbrOfGenotypeGroups: int 3 689s .. .. ..$ tau : num [1:2] 0.315 0.677 689s .. .. ..$ n : int 14640 689s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 689s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 689s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 689s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 689s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 689s .. .. .. ..$ type : chr [1:2] "valley" "valley" 689s .. .. .. ..$ x : num [1:2] 0.315 0.677 689s .. .. .. ..$ density: num [1:2] 0.522 0.552 689s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 689s Setup up data...done 689s Dropping loci for which TCNs are missing... 689s Number of loci dropped: 12 689s Dropping loci for which TCNs are missing...done 689s Ordering data along genome... 689s 'data.frame': 14658 obs. of 7 variables: 689s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 689s $ x : num 554484 730720 782343 878522 916294 ... 689s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 689s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 689s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 689s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 689s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 689s Ordering data along genome...done 689s Keeping only current chromosome for 'knownSegments'... 689s Chromosome: 1 689s Known segments for this chromosome: 689s chromosome start end length 689s 1 1 -Inf 120992603 Inf 689s 2 1 120992604 141510002 20517398 689s 3 1 141510003 Inf Inf 689s Keeping only current chromosome for 'knownSegments'...done 689s alphaTCN: 0.009 689s alphaDH: 0.001 689s Number of loci: 14658 689s Calculating DHs... 689s Number of SNPs: 14658 689s Number of heterozygous SNPs: 4196 (28.63%) 689s Normalized DHs: 689s num [1:14658] NA NA NA NA NA ... 689s Calculating DHs...done 689s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 689s Produced 2 seeds from this stream for future usage 689s Identification of change points by total copy numbers... 689s Segmenting by CBS... 689s Chromosome: 1 689s Segmenting multiple segments on current chromosome... 689s Number of segments: 3 689s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 689s Produced 3 seeds from this stream for future usage 689s Segmenting by CBS... 689s Chromosome: 1 689s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 689s Segmenting by CBS...done 689s Segmenting by CBS... 689s Chromosome: 1 689s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 689s Segmenting by CBS...done 689s Segmenting multiple segments on current chromosome...done 689s Segmenting by CBS...done 689s List of 4 689s $ data :'data.frame': 14658 obs. of 4 variables: 689s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 689s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 689s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 689s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 689s $ output :'data.frame': 4 obs. of 6 variables: 689s ..$ sampleName: chr [1:4] NA NA NA NA 689s ..$ chromosome: int [1:4] 1 1 1 1 689s ..$ start : num [1:4] 5.54e+05 1.21e+08 1.42e+08 1.85e+08 689s ..$ end : num [1:4] 1.21e+08 1.42e+08 1.85e+08 2.47e+08 689s ..$ nbrOfLoci : int [1:4] 7586 0 2681 4391 689s ..$ mean : num [1:4] 1.39 NA 2.07 2.63 689s $ segRows:'data.frame': 4 obs. of 2 variables: 689s ..$ startRow: int [1:4] 1 NA 7587 10268 689s ..$ endRow : int [1:4] 7586 NA 10267 14658 689s $ params :List of 5 689s ..$ alpha : num 0.009 689s ..$ undo : num 0 689s ..$ joinSegments : logi TRUE 689s ..$ knownSegments:'data.frame': 4 obs. of 3 variables: 689s .. ..$ chromosome: int [1:4] 1 1 2 1 689s .. ..$ start : num [1:4] -Inf -Inf -Inf 1.42e+08 689s .. ..$ end : num [1:4] 1.21e+08 Inf Inf Inf 689s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 689s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 689s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.53 0.002 0.533 0 0 689s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 689s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 689s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 689s Identification of change points by total copy numbers...done 689s Restructure TCN segmentation results... 689s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 689s 1 1 554484 120992603 7586 1.3853 689s 2 1 120992604 141510002 0 NA 689s 3 1 141510003 185449813 2681 2.0689 689s 4 1 185449813 247137334 4391 2.6341 689s Number of TCN segments: 4 689s Restructure TCN segmentation results...done 689s Total CN segment #1 ([ 554484,1.20993e+08]) of 4... 689s Number of TCN loci in segment: 7586 689s Locus data for TCN segment: 689s 'data.frame': 7586 obs. of 9 variables: 689s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 689s $ x : num 554484 730720 782343 878522 916294 ... 689s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 689s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 689s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 689s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 689s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 689s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 689s $ rho : num NA NA NA NA NA ... 689s Number of loci: 7586 689s Number of SNPs: 2108 (27.79%) 689s Number of heterozygous SNPs: 2108 (100.00%) 689s Chromosome: 1 689s Segmenting DH signals... 689s Segmenting by CBS... 689s Chromosome: 1 689s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 689s Segmenting by CBS...done 689s List of 4 689s $ data :'data.frame': 7586 obs. of 4 variables: 689s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 689s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 689s ..$ y : num [1:7586] NA NA NA NA NA ... 689s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 689s $ output :'data.frame': 1 obs. of 6 variables: 689s ..$ sampleName: chr NA 689s ..$ chromosome: int 1 689s ..$ start : num 554484 689s ..$ end : num 1.21e+08 689s ..$ nbrOfLoci : int 2108 689s ..$ mean : num 0.512 689s $ segRows:'data.frame': 1 obs. of 2 variables: 689s ..$ startRow: int 10 689s ..$ endRow : int 7574 689s $ params :List of 5 689s ..$ alpha : num 0.001 689s ..$ undo : num 0 689s ..$ joinSegments : logi TRUE 689s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 689s .. ..$ chromosome: int 1 689s .. ..$ start : num 554484 689s .. ..$ end : num 1.21e+08 689s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 689s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 689s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.114 0.004 0.118 0 0 689s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 689s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 689s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 689s DH segmentation (locally-indexed) rows: 689s startRow endRow 689s 1 10 7574 689s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 689s DH segmentation rows: 689s startRow endRow 689s 1 10 7574 689s Segmenting DH signals...done 689s DH segmentation table: 689s dhStart dhEnd dhNbrOfLoci dhMean 689s 1 554484 120992603 2108 0.5116 689s startRow endRow 689s 1 10 7574 689s Rows: 689s [1] 1 689s TCN segmentation rows: 689s startRow endRow 689s 1 1 7586 689s TCN and DH segmentation rows: 689s startRow endRow 689s 1 1 7586 689s startRow endRow 689s 1 10 7574 689s NULL 689s TCN segmentation (expanded) rows: 689s startRow endRow 689s 1 1 7586 689s TCN and DH segmentation rows: 689s startRow endRow 689s 1 1 7586 689s 2 NA NA 689s 3 7587 10267 689s 4 10268 14658 689s startRow endRow 689s 1 10 7574 689s startRow endRow 689s 1 1 7586 689s Total CN segmentation table (expanded): 689s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 689s 1 1 554484 120992603 7586 1.3853 2108 2108 689s (TCN,DH) segmentation for one total CN segment: 689s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 1 1 1 1 554484 120992603 7586 1.3853 2108 689s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 689s 1 2108 554484 120992603 2108 0.5116 689s Total CN segment #1 ([ 554484,1.20993e+08]) of 4...done 689s Total CN segment #2 ([1.20993e+08,1.4151e+08]) of 4... 689s Number of TCN loci in segment: 0 689s Locus data for TCN segment: 689s 'data.frame': 0 obs. of 9 variables: 689s $ chromosome: int 689s $ x : num 689s $ CT : num 689s $ betaT : num 689s $ betaTN : num 689s $ betaN : num 689s $ muN : num 689s $ index : int 689s $ rho : num 689s Number of loci: 0 689s Number of SNPs: 0 (NaN%) 689s Number of heterozygous SNPs: 0 (NaN%) 689s Chromosome: 1 689s Segmenting DH signals... 689s Segmenting by CBS... 689s Chromosome: NA 689s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 689s Segmenting by CBS...done 689s List of 4 689s $ data :'data.frame': 0 obs. of 4 variables: 689s ..$ chromosome: int(0) 689s ..$ x : num(0) 689s ..$ y : num(0) 689s ..$ index : int(0) 689s $ output :'data.frame': 0 obs. of 6 variables: 689s ..$ sampleName: chr(0) 689s ..$ chromosome: num(0) 689s ..$ start : num(0) 689s ..$ end : num(0) 689s ..$ nbrOfLoci : int(0) 689s ..$ mean : num(0) 689s $ segRows:'data.frame': 0 obs. of 2 variables: 689s ..$ startRow: int(0) 689s ..$ endRow : int(0) 689s $ params :List of 5 689s ..$ alpha : num 0.001 689s ..$ undo : num 0 689s ..$ joinSegments : logi TRUE 689s ..$ knownSegments:'data.frame': 0 obs. of 3 variables: 689s .. ..$ chromosome: int(0) 689s .. ..$ start : num(0) 689s .. ..$ end : num(0) 689s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 689s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 689s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.008 0 0.009 0 0 689s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 689s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 689s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 689s DH segmentation (locally-indexed) rows: 689s [1] startRow endRow 689s <0 rows> (or 0-length row.names) 689s int(0) 689s DH segmentation rows: 689s [1] startRow endRow 689s <0 rows> (or 0-length row.names) 689s Segmenting DH signals...done 689s DH segmentation table: 689s dhStart dhEnd dhNbrOfLoci dhMean 689s NA NA NA NA NA 689s startRow endRow 689s NA NA NA 689s Rows: 689s [1] 2 689s TCN segmentation rows: 689s startRow endRow 689s 2 NA NA 689s TCN and DH segmentation rows: 689s startRow endRow 689s 2 NA NA 689s startRow endRow 689s NA NA NA 689s startRow endRow 689s 1 1 7586 689s TCN segmentation (expanded) rows: 689s startRow endRow 689s 1 1 7586 689s 2 NA NA 689s TCN and DH segmentation rows: 689s startRow endRow 689s 1 1 7586 689s 2 NA NA 689s 3 7587 10267 689s 4 10268 14658 689s startRow endRow 689s 1 10 7574 689s 2 NA NA 689s startRow endRow 689s 1 1 7586 689s 2 NA NA 689s Total CN segmentation table (expanded): 689s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 689s 2 1 120992604 141510002 0 NA 0 0 689s (TCN,DH) segmentation for one total CN segment: 689s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 2 2 1 1 120992604 141510002 0 NA 0 689s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 689s 2 0 NA NA NA NA 689s Total CN segment #2 ([1.20993e+08,1.4151e+08]) of 4...done 689s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4... 689s Number of TCN loci in segment: 2681 689s Locus data for TCN segment: 689s 'data.frame': 2681 obs. of 9 variables: 689s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 689s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 689s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 689s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 689s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 689s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 689s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 689s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 689s $ rho : num 0.117 0.258 NA NA NA ... 689s Number of loci: 2681 689s Number of SNPs: 777 (28.98%) 689s Number of heterozygous SNPs: 777 (100.00%) 689s Chromosome: 1 689s Segmenting DH signals... 689s Segmenting by CBS... 689s Chromosome: 1 689s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 689s Segmenting by CBS...done 689s List of 4 689s $ data :'data.frame': 2681 obs. of 4 variables: 689s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 689s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 689s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 689s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 689s $ output :'data.frame': 1 obs. of 6 variables: 689s ..$ sampleName: chr NA 689s ..$ chromosome: int 1 689s ..$ start : num 1.42e+08 689s ..$ end : num 1.85e+08 689s ..$ nbrOfLoci : int 777 689s ..$ mean : num 0.0973 689s $ segRows:'data.frame': 1 obs. of 2 variables: 689s ..$ startRow: int 1 689s ..$ endRow : int 2677 689s $ params :List of 5 689s ..$ alpha : num 0.001 689s ..$ undo : num 0 689s ..$ joinSegments : logi TRUE 689s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 689s .. ..$ chromosome: int 1 689s .. ..$ start : num 1.42e+08 689s .. ..$ end : num 1.85e+08 689s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 689s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 689s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.029 0 0.028 0 0 689s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 689s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 689s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 689s DH segmentation (locally-indexed) rows: 689s startRow endRow 689s 1 1 2677 689s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 689s DH segmentation rows: 689s startRow endRow 689s 1 7587 10263 689s Segmenting DH signals...done 689s DH segmentation table: 689s dhStart dhEnd dhNbrOfLoci dhMean 689s 1 141510003 185449813 777 0.0973 689s startRow endRow 689s 1 7587 10263 689s Rows: 689s [1] 3 689s TCN segmentation rows: 689s startRow endRow 689s 3 7587 10267 689s TCN and DH segmentation rows: 689s startRow endRow 689s 3 7587 10267 689s startRow endRow 689s 1 7587 10263 689s startRow endRow 689s 1 1 7586 689s 2 NA NA 689s TCN segmentation (expanded) rows: 689s startRow endRow 689s 1 1 7586 689s 2 NA NA 689s 3 7587 10267 689s TCN and DH segmentation rows: 689s startRow endRow 689s 1 1 7586 689s 2 NA NA 689s 3 7587 10267 689s 4 10268 14658 689s startRow endRow 689s 1 10 7574 689s 2 NA NA 689s 3 7587 10263 689s startRow endRow 689s 1 1 7586 689s 2 NA NA 689s 3 7587 10267 689s Total CN segmentation table (expanded): 689s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 689s 3 1 141510003 185449813 2681 2.0689 777 777 689s (TCN,DH) segmentation for one total CN segment: 689s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 3 3 1 1 141510003 185449813 2681 2.0689 777 689s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 689s 3 777 141510003 185449813 777 0.0973 689s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4...done 689s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4... 689s Number of TCN loci in segment: 4391 689s Locus data for TCN segment: 689s 'data.frame': 4391 obs. of 9 variables: 689s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 689s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 689s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 689s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 689s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 689s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 689s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 689s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 689s $ rho : num NA 0.2186 NA 0.0503 NA ... 689s Number of loci: 4391 689s Number of SNPs: 1311 (29.86%) 689s Number of heterozygous SNPs: 1311 (100.00%) 689s Chromosome: 1 689s Segmenting DH signals... 689s Segmenting by CBS... 689s Chromosome: 1 689s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 689s Segmenting by CBS...done 689s List of 4 689s $ data :'data.frame': 4391 obs. of 4 variables: 689s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 689s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 689s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 689s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 689s $ output :'data.frame': 1 obs. of 6 variables: 689s ..$ sampleName: chr NA 689s ..$ chromosome: int 1 689s ..$ start : num 1.85e+08 689s ..$ end : num 2.47e+08 689s ..$ nbrOfLoci : int 1311 689s ..$ mean : num 0.23 689s $ segRows:'data.frame': 1 obs. of 2 variables: 689s ..$ startRow: int 2 689s ..$ endRow : int 4388 689s $ params :List of 5 689s ..$ alpha : num 0.001 689s ..$ undo : num 0 689s ..$ joinSegments : logi TRUE 689s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 689s .. ..$ chromosome: int 1 689s .. ..$ start : num 1.85e+08 689s .. ..$ end : num 2.47e+08 689s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 689s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 689s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.073 0.001 0.073 0 0 689s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 689s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 689s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 689s DH segmentation (locally-indexed) rows: 689s startRow endRow 689s 1 2 4388 689s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 689s DH segmentation rows: 689s startRow endRow 689s 1 10269 14655 689s Segmenting DH signals...done 689s DH segmentation table: 689s dhStart dhEnd dhNbrOfLoci dhMean 689s 1 185449813 247137334 1311 0.2295 689s startRow endRow 689s 1 10269 14655 689s Rows: 689s [1] 4 689s TCN segmentation rows: 689s startRow endRow 689s 4 10268 14658 689s TCN and DH segmentation rows: 689s startRow endRow 689s 4 10268 14658 689s startRow endRow 689s 1 10269 14655 689s startRow endRow 689s 1 1 7586 689s 2 NA NA 689s 3 7587 10267 689s TCN segmentation (expanded) rows: 689s startRow endRow 689s 1 1 7586 689s 2 NA NA 689s 3 7587 10267 689s 4 10268 14658 689s TCN and DH segmentation rows: 689s startRow endRow 689s 1 1 7586 689s 2 NA NA 689s 3 7587 10267 689s 4 10268 14658 689s startRow endRow 689s 1 10 7574 689s 2 NA NA 689s 3 7587 10263 689s 4 10269 14655 689s startRow endRow 689s 1 1 7586 689s 2 NA NA 689s 3 7587 10267 689s 4 10268 14658 689s Total CN segmentation table (expanded): 689s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 689s 4 1 185449813 247137334 4391 2.6341 1311 1311 689s (TCN,DH) segmentation for one total CN segment: 689s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 4 4 1 1 185449813 247137334 4391 2.6341 1311 689s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 689s 4 1311 185449813 247137334 1311 0.2295 689s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4...done 689s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 1 1 1 1 554484 120992603 7586 1.3853 2108 689s 2 1 2 1 120992604 141510002 0 NA 0 689s 3 1 3 1 141510003 185449813 2681 2.0689 777 689s 4 1 4 1 185449813 247137334 4391 2.6341 1311 689s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 689s 1 2108 554484 120992603 2108 0.5116 689s 2 0 NA NA NA NA 689s 3 777 141510003 185449813 777 0.0973 689s 4 1311 185449813 247137334 1311 0.2295 689s Calculating (C1,C2) per segment... 689s Calculating (C1,C2) per segment...done 689s Number of segments: 4 689s Segmenting paired tumor-normal signals using Paired PSCBS...done 689s Post-segmenting TCNs... 689s Number of segments: 4 689s Number of chromosomes: 1 689s [1] 1 689s Chromosome 1 ('chr01') of 1... 689s Rows: 689s [1] 1 2 3 4 689s Number of segments: 4 689s TCN segment #1 ('1') of 4... 689s Nothing todo. Only one DH segmentation. Skipping. 689s TCN segment #1 ('1') of 4...done 689s TCN segment #2 ('2') of 4... 689s Nothing todo. Only one DH segmentation. Skipping. 689s TCN segment #2 ('2') of 4...done 689s TCN segment #3 ('3') of 4... 689s Nothing todo. Only one DH segmentation. Skipping. 689s TCN segment #3 ('3') of 4...done 689s TCN segment #4 ('4') of 4... 689s Nothing todo. Only one DH segmentation. Skipping. 689s TCN segment #4 ('4') of 4...done 689s Chromosome 1 ('chr01') of 1...done 689s Update (C1,C2) per segment... 689s Update (C1,C2) per segment...done 689s Post-segmenting TCNs...done 689s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 1 1 1 1 554484 120992603 7586 1.3853 2108 689s 2 1 2 1 120992604 141510002 0 NA 0 689s 3 1 3 1 141510003 185449813 2681 2.0689 777 689s 4 1 4 1 185449813 247137334 4391 2.6341 1311 689s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 689s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 689s 2 0 NA NA NA NA NA NA 689s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 689s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 689s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 1 1 1 1 554484 120992603 7586 1.3853 2108 689s 2 1 2 1 120992604 141510002 0 NA 0 689s 3 1 3 1 141510003 185449813 2681 2.0689 777 689s 4 1 4 1 185449813 247137334 4391 2.6341 1311 689s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 689s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 689s 2 0 NA NA NA NA NA NA 689s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 689s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 689s > print(fit) 689s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 1 1 1 1 554484 120992603 7586 1.3853 2108 689s 2 1 2 1 120992604 141510002 0 NA 0 689s 3 1 3 1 141510003 185449813 2681 2.0689 777 689s 4 1 4 1 185449813 247137334 4391 2.6341 1311 689s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 689s 1 2108 2108 0.5116 0.3382903 1.047010 689s 2 0 NA NA NA NA 689s 3 777 777 0.0973 0.9337980 1.135102 689s 4 1311 1311 0.2295 1.0147870 1.619313 689s > 689s > # Plot results 689s > plotTracks(fit) 689s > 689s > # Sanity check 689s > stopifnot(nbrOfSegments(fit) == nSegs) 689s > 689s > 689s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 689s > # Bootstrap segment level estimates 689s > # (used by the AB caller, which, if skipped here, 689s > # will do it automatically) 689s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 689s > fit <- bootstrapTCNandDHByRegion(fit, B=B, verbose=-10) 689s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint... 689s Already done? 689s tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% dh_97.5% 689s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 689s c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% c2_97.5% 689s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 689s Bootstrapping (TCN,DH,C1,C2) segment mean levels... 689s Icat segmentByPairedPSCBS,calls.Rout 689s + [ 0 != 0 ] 689s + echo Test segmentByPairedPSCBS,calls passed 689s + echo 0 689s + echo Begin test segmentByPairedPSCBS,futures 689s + exitcode=0 689s + R CMD BATCH segmentByPairedPSCBS,futures.R 689s dentifying heterozygous & homozygous SNPs and non-polymorphic loci... 689s Number of loci: 14658 689s Number of SNPs: 4196 689s Number of non-SNPs: 10462 689s Identifying heterozygous & homozygous SNPs and non-polymorphic loci...done 689s num [1:4, 1:100, 1:4] NA NA NA NA NA NA NA NA NA NA ... 689s - attr(*, "dimnames")=List of 3 689s ..$ : NULL 689s ..$ : NULL 689s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 689s Segment #1 (chr 1, tcnId=1, dhId=1) of 4... 689s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 1 1 1 1 554484 120992603 7586 1.3853 2108 689s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 689s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.04701 689s Number of TCNs: 7586 689s Number of DHs: 2108 689s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 689s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 689s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 689s Identify loci used to bootstrap DH means... 689s Heterozygous SNPs to resample for DH: 689s int [1:2108] 10 12 24 28 31 33 34 39 46 48 ... 689s Identify loci used to bootstrap DH means...done 689s Identify loci used to bootstrap TCN means... 689s SNPs: 689s int [1:2108] 10 12 24 28 31 33 34 39 46 48 ... 689s Non-polymorphic loci: 689s int [1:5478] 1 2 3 4 5 6 7 8 9 11 ... 689s Heterozygous SNPs to resample for TCN: 689s int [1:2108] 10 12 24 28 31 33 34 39 46 48 ... 689s Homozygous SNPs to resample for TCN: 689s int(0) 689s Non-polymorphic loci to resample for TCN: 689s int [1:5478] 1 2 3 4 5 6 7 8 9 11 ... 689s Heterozygous SNPs with non-DH to resample for TCN: 689s int(0) 689s Loci to resample for TCN: 689s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 689s Identify loci used to bootstrap TCN means...done 689s Number of (#hets, #homs, #nonSNPs): (2108,0,5478) 689s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 689s Number of bootstrap samples: 100 689s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 689s Segment #1 (chr 1, tcnId=1, dhId=1) of 4...done 689s Segment #2 (chr 1, tcnId=2, dhId=1) of 4... 689s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 2 1 2 1 120992604 141510002 0 NA 0 689s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 689s 2 0 NA NA 0 NA NA NA 689s Number of TCNs: 0 689s Number of DHs: 0 689s int 0 689s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 689s int(0) 689s Identify loci used to bootstrap DH means... 689s Heterozygous SNPs to resample for DH: 689s int 0 689s Identify loci used to bootstrap DH means...done 689s Identify loci used to bootstrap TCN means... 689s SNPs: 689s int(0) 689s Non-polymorphic loci: 689s int(0) 689s Heterozygous SNPs to resample for TCN: 689s int(0) 689s Homozygous SNPs to resample for TCN: 689s int(0) 689s Non-polymorphic loci to resample for TCN: 689s int(0) 689s Heterozygous SNPs with non-DH to resample for TCN: 689s int(0) 689s Loci to resample for TCN: 689s int(0) 689s Identify loci used to bootstrap TCN means...done 689s Number of (#hets, #homs, #nonSNPs): (0,0,0) 689s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 689s Number of bootstrap samples: 100 689s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 689s Segment #2 (chr 1, tcnId=2, dhId=1) of 4...done 689s Segment #3 (chr 1, tcnId=3, dhId=1) of 4... 689s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 3 1 3 1 141510003 185449813 2681 2.0689 777 689s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 689s 3 777 141510003 185449813 777 0.0973 0.933798 1.135102 689s Number of TCNs: 2681 689s Number of DHs: 777 689s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 689s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 689s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 689s Identify loci used to bootstrap DH means... 689s Heterozygous SNPs to resample for DH: 689s int [1:777] 7587 7588 7594 7614 7616 7626 7627 7628 7635 7638 ... 689s Identify loci used to bootstrap DH means...done 689s Identify loci used to bootstrap TCN means... 689s SNPs: 689s int [1:777] 7587 7588 7594 7614 7616 7626 7627 7628 7635 7638 ... 689s Non-polymorphic loci: 689s int [1:1904] 7589 7590 7591 7592 7593 7595 7596 7597 7598 7599 ... 689s Heterozygous SNPs to resample for TCN: 689s int [1:777] 7587 7588 7594 7614 7616 7626 7627 7628 7635 7638 ... 689s Homozygous SNPs to resample for TCN: 689s int(0) 689s Non-polymorphic loci to resample for TCN: 689s int [1:1904] 7589 7590 7591 7592 7593 7595 7596 7597 7598 7599 ... 689s Heterozygous SNPs with non-DH to resample for TCN: 689s int(0) 689s Loci to resample for TCN: 689s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 689s Identify loci used to bootstrap TCN means...done 689s Number of (#hets, #homs, #nonSNPs): (777,0,1904) 689s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 689s Number of bootstrap samples: 100 689s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 689s Segment #3 (chr 1, tcnId=3, dhId=1) of 4...done 689s Segment #4 (chr 1, tcnId=4, dhId=1) of 4... 689s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 4 1 4 1 185449813 247137334 4391 2.6341 1311 689s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 689s 4 1311 185449813 247137334 1311 0.2295 1.014787 1.619313 689s Number of TCNs: 4391 689s Number of DHs: 1311 689s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 689s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 689s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 689s Identify loci used to bootstrap DH means... 689s Heterozygous SNPs to resample for DH: 689s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 689s Identify loci used to bootstrap DH means...done 689s Identify loci used to bootstrap TCN means... 689s SNPs: 689s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 689s Non-polymorphic loci: 689s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 689s Heterozygous SNPs to resample for TCN: 689s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 689s Homozygous SNPs to resample for TCN: 689s int(0) 689s Non-polymorphic loci to resample for TCN: 689s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 689s Heterozygous SNPs with non-DH to resample for TCN: 689s int(0) 689s Loci to resample for TCN: 689s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 689s Identify loci used to bootstrap TCN means...done 689s Number of (#hets, #homs, #nonSNPs): (1311,0,3080) 689s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 689s Number of bootstrap samples: 100 689s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 689s Segment #4 (chr 1, tcnId=4, dhId=1) of 4...done 689s Bootstrapped segment mean levels 689s num [1:4, 1:100, 1:4] 1.39 NA 2.08 2.63 1.38 ... 689s - attr(*, "dimnames")=List of 3 689s ..$ : NULL 689s ..$ : NULL 689s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 689s Calculating (C1,C2) mean levels from (TCN,DH) mean levels... 689s num [1:4, 1:100, 1:4] 1.39 NA 2.08 2.63 1.38 ... 689s - attr(*, "dimnames")=List of 3 689s ..$ : NULL 689s ..$ : NULL 689s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 689s Calculating (C1,C2) mean levels from (TCN,DH) mean levels...done 689s Calculating polar (alpha,radius,manhattan) for change points... 689s num [1:3, 1:100, 1:2] NA NA -0.0752 NA NA ... 689s - attr(*, "dimnames")=List of 3 689s ..$ : NULL 689s ..$ : NULL 689s ..$ : chr [1:2] "c1" "c2" 689s Bootstrapped change points 689s num [1:3, 1:100, 1:5] NA NA -1.73 NA NA ... 689s - attr(*, "dimnames")=List of 3 689s ..$ : NULL 689s ..$ : NULL 689s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 689s Calculating polar (alpha,radius,manhattan) for change points...done 689s Bootstrapping (TCN,DH,C1,C2) segment mean levels...done 689s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data... 689s num [1:4, 1:4, 1:4] NA NA NA NA NA NA NA NA NA NA ... 689s - attr(*, "dimnames")=List of 3 689s ..$ : NULL 689s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 689s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 689s Field #1 ('tcn') of 4... 689s Segment #1 of 4... 689s Segment #1 of 4...done 689s Segment #2 of 4... 689s Segment #2 of 4...done 689s Segment #3 of 4... 689s Segment #3 of 4...done 689s Segment #4 of 4... 689s Segment #4 of 4...done 689s Field #1 ('tcn') of 4...done 689s Field #2 ('dh') of 4... 689s Segment #1 of 4... 689s Segment #1 of 4...done 689s Segment #2 of 4... 689s Segment #2 of 4...done 689s Segment #3 of 4... 689s Segment #3 of 4...done 689s Segment #4 of 4... 689s Segment #4 of 4...done 689s Field #2 ('dh') of 4...done 689s Field #3 ('c1') of 4... 689s Segment #1 of 4... 689s Segment #1 of 4...done 689s Segment #2 of 4... 689s Segment #2 of 4...done 689s Segment #3 of 4... 689s Segment #3 of 4...done 689s Segment #4 of 4... 689s Segment #4 of 4...done 689s Field #3 ('c1') of 4...done 689s Field #4 ('c2') of 4... 689s Segment #1 of 4... 689s Segment #1 of 4...done 689s Segment #2 of 4... 689s Segment #2 of 4...done 689s Segment #3 of 4... 689s Segment #3 of 4...done 689s Segment #4 of 4... 689s Segment #4 of 4...done 689s Field #4 ('c2') of 4...done 689s Bootstrap statistics 689s num [1:4, 1:4, 1:4] 1.38 NA 2.06 2.63 1.38 ... 689s - attr(*, "dimnames")=List of 3 689s ..$ : NULL 689s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 689s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 689s Statistical sanity checks (iff B >= 100)... 689s Available summaries: 2.5%, 5%, 95%, 97.5% 689s Available quantiles: 0.025, 0.05, 0.95, 0.975 689s num [1:4, 1:4, 1:4] 1.38 NA 2.06 2.63 1.38 ... 689s - attr(*, "dimnames")=List of 3 689s ..$ : NULL 689s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 689s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 689s Field #1 ('tcn') of 4... 689s Seg 1. mean=1.3853, range=[1.37909,1.39287], n=7586 689s Seg 2. mean=NA, range=[NA,NA], n=0 689s Seg 3. mean=2.0689, range=[2.05903,2.079], n=2681 689s Seg 4. mean=2.6341, range=[2.62504,2.64649], n=4391 689s Field #1 ('tcn') of 4...done 689s Field #2 ('dh') of 4... 689s Seg 1. mean=0.5116, range=[0.502148,0.519941], n=2108 689s Seg 2. mean=NA, range=[NA,NA], n=NA 689s Seg 3. mean=0.0973, range=[0.0906366,0.105818], n=777 689s Seg 4. mean=0.2295, range=[0.222919,0.237005], n=1311 689s Field #2 ('dh') of 4...done 689s Field #3 ('c1') of 4... 689s Seg 1. mean=0.33829, range=[0.332209,0.345936], n=2108 689s Seg 2. mean=NA, range=[NA,NA], n=NA 689s Seg 3. mean=0.933798, range=[0.924112,0.941776], n=777 689s Seg 4. mean=1.01479, range=[1.00381,1.02461], n=1311 689s Field #3 ('c1') of 4...done 689s Field #4 ('c2') of 4... 689s Seg 1. mean=1.04701, range=[1.03882,1.05318], n=2108 689s Seg 2. mean=NA, range=[NA,NA], n=NA 689s Seg 3. mean=1.1351, range=[1.12454,1.1465], n=777 689s Seg 4. mean=1.61931, range=[1.60862,1.63328], n=1311 689s Field #4 ('c2') of 4...done 689s Statistical sanity checks (iff B >= 100)...done 689s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data...done 689s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data... 689s num [1:3, 1:4, 1:5] NA NA NA NA NA NA NA NA NA NA ... 689s - attr(*, "dimnames")=List of 3 689s ..$ : NULL 689s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 689s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 689s Field #1 ('alpha') of 5... 689s Changepoint #1 of 3... 689s Changepoint #1 of 3...done 689s Changepoint #2 of 3... 689s Changepoint #2 of 3...done 689s Changepoint #3 of 3... 689s Changepoint #3 of 3...done 689s Field #1 ('alpha') of 5...done 689s Field #2 ('radius') of 5... 689s Changepoint #1 of 3... 689s Changepoint #1 of 3...done 689s Changepoint #2 of 3... 689s Changepoint #2 of 3...done 689s Changepoint #3 of 3... 689s Changepoint #3 of 3...done 689s Field #2 ('radius') of 5...done 689s Field #3 ('manhattan') of 5... 689s Changepoint #1 of 3... 689s Changepoint #1 of 3...done 689s Changepoint #2 of 3... 689s Changepoint #2 of 3...done 689s Changepoint #3 of 3... 689s Changepoint #3 of 3...done 689s Field #3 ('manhattan') of 5...done 689s Field #4 ('d1') of 5... 689s Changepoint #1 of 3... 689s Changepoint #1 of 3...done 689s Changepoint #2 of 3... 689s Changepoint #2 of 3...done 689s Changepoint #3 of 3... 689s Changepoint #3 of 3...done 689s Field #4 ('d1') of 5...done 689s Field #5 ('d2') of 5... 689s Changepoint #1 of 3... 689s Changepoint #1 of 3...done 689s Changepoint #2 of 3... 689s Changepoint #2 of 3...done 689s Changepoint #3 of 3... 689s Changepoint #3 of 3...done 689s Field #5 ('d2') of 5...done 689s Bootstrap statistics 689s num [1:3, 1:4, 1:5] NA NA -1.77 NA NA ... 689s - attr(*, "dimnames")=List of 3 689s ..$ : NULL 689s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 689s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 689s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data...done 689s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint...done 689s > print(fit) 689s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 1 1 1 1 554484 120992603 7586 1.3853 2108 689s 2 1 2 1 120992604 141510002 0 NA 0 689s 3 1 3 1 141510003 185449813 2681 2.0689 777 689s 4 1 4 1 185449813 247137334 4391 2.6341 1311 689s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 689s 1 2108 2108 0.5116 0.3382903 1.047010 689s 2 0 NA NA NA NA 689s 3 777 777 0.0973 0.9337980 1.135102 689s 4 1311 1311 0.2295 1.0147870 1.619313 689s > plotTracks(fit) 689s > 689s > 689s > 689s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 689s > # Calling segments with run of homozygosity (ROH) 689s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 689s > fit <- callROH(fit, verbose=-10) 689s Calling ROH... 689s Segment #1 of 4... 689s Calling ROH for a single segment... 689s Number of SNPs: 7586 689s Calling ROH for a single segment...done 689s Segment #1 of 4...done 689s Segment #2 of 4... 689s Calling ROH for a single segment... 689s Number of SNPs: 0 689s Calling ROH for a single segment...done 689s Segment #2 of 4...done 689s Segment #3 of 4... 689s Calling ROH for a single segment... 689s Number of SNPs: 2681 689s Calling ROH for a single segment...done 689s Segment #3 of 4...done 689s Segment #4 of 4... 689s Calling ROH for a single segment... 689s Number of SNPs: 4391 689s Calling ROH for a single segment...done 689s Segment #4 of 4...done 689s ROH calls: 689s logi [1:4] FALSE NA FALSE FALSE 689s Mode FALSE NA's 689s logical 3 1 689s Calling ROH...done 689s > print(fit) 689s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 1 1 1 1 554484 120992603 7586 1.3853 2108 689s 2 1 2 1 120992604 141510002 0 NA 0 689s 3 1 3 1 141510003 185449813 2681 2.0689 777 689s 4 1 4 1 185449813 247137334 4391 2.6341 1311 689s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean rohCall 689s 1 2108 2108 0.5116 0.3382903 1.047010 FALSE 689s 2 0 NA NA NA NA NA 689s 3 777 777 0.0973 0.9337980 1.135102 FALSE 689s 4 1311 1311 0.2295 1.0147870 1.619313 FALSE 689s > plotTracks(fit) 689s > 689s > 689s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 689s > # Estimate background 689s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 689s > kappa <- estimateKappa(fit, verbose=-10) 689s Estimate global background (including normal contamination and more)... 689s Number of segments: 3 689s Estimating threshold Delta0.5 from the empirical density of C1:s... 689s adjust: 1 689s minDensity: 0.2 689s ploidy: 2 689s All peaks: 689s type x density 689s 1 peak 0.3362194 1.101272 689s 3 peak 0.9811492 1.065711 689s C1=0 and C1=1 peaks: 689s type x density 689s 1 peak 0.3362194 1.101272 689s 3 peak 0.9811492 1.065711 689s Estimate of Delta0.5: 0.65868427808456 689s Estimating threshold Delta0.5 from the empirical density of C1:s...done 689s Number of segments with C1 < Delta0.5: 1 689s Estimate of kappa: 0.33829026 689s Estimate global background (including normal contamination and more)...done 689s Warning message: 689s In density.default(c1, weights = weights, adjust = adjust, from = from, : 689s Selecting bandwidth *not* using 'weights' 689s > print(kappa) 689s [1] 0.3382903 689s > ## [1] 0.226011 689s > 689s > 689s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 689s > # Calling segments in allelic balance (AB) 689s > # NOTE: Ideally, this should be done on whole-genome data 689s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 689s > # Explicitly estimate the threshold in DH for calling AB 689s > # (which be done by default by the caller, if skipped here) 689s > deltaAB <- estimateDeltaAB(fit, flavor="qq(DH)", verbose=-10) 689s Estimating DH threshold for calling allelic imbalances... 689s flavor: qq(DH) 689s scale: 1 689s Estimating DH threshold for AB caller... 689s quantile #1: 0.05 689s Symmetric quantile #2: 0.9 689s Number of segments: 3 689s Weighted 5% quantile of DH: 0.257710 689s Number of segments with small DH: 2 689s Number of data points: 7072 689s Number of finite data points: 2088 689s Estimate of (1-0.9):th and 50% quantiles: (0.0310411,0.163658) 689s Estimate of 0.9:th "symmetric" quantile: 0.296275 689s Estimating DH threshold for AB caller...done 689s Estimated delta: 0.296 689s Estimating DH threshold for calling allelic imbalances...done 689s > if (Sys.getenv("_R_CHECK_FULL_") == "") { 689s + # Ad hoc workaround for not utilizing all of the data 689s + # in the test, which results in a poor estimate 689s + deltaAB <- 0.165 689s + } 689s > print(deltaAB) 689s [1] 0.165 689s > ## [1] 0.1657131 689s > 689s > fit <- callAB(fit, delta=deltaAB, verbose=-10) 689s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 689s delta (offset adjusting for bias in DH): 0.165 689s alpha (CI quantile; significance level): 0.05 689s Calling segments... 689s Number of segments called allelic balance (AB): 1 (25.00%) of 4 689s Calling segments...done 689s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 689s > print(fit) 689s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 1 1 1 1 554484 120992603 7586 1.3853 2108 689s 2 1 2 1 120992604 141510002 0 NA 0 689s 3 1 3 1 141510003 185449813 2681 2.0689 777 689s 4 1 4 1 185449813 247137334 4391 2.6341 1311 689s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean rohCall abCall 689s 1 2108 2108 0.5116 0.3382903 1.047010 FALSE FALSE 689s 2 0 NA NA NA NA NA NA 689s 3 777 777 0.0973 0.9337980 1.135102 FALSE TRUE 689s 4 1311 1311 0.2295 1.0147870 1.619313 FALSE FALSE 689s > plotTracks(fit) 689s > 689s > # Even if not explicitly specified, the estimated 689s > # threshold parameter is returned by the caller 689s > stopifnot(fit$params$deltaAB == deltaAB) 689s > 689s > 689s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 689s > # Calling segments in loss-of-heterozygosity (LOH) 689s > # NOTE: Ideally, this should be done on whole-genome data 689s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 689s > # Explicitly estimate the threshold in C1 for calling LOH 689s > # (which be done by default by the caller, if skipped here) 689s > deltaLOH <- estimateDeltaLOH(fit, flavor="minC1|nonAB", verbose=-10) 689s Estimating DH threshold for calling LOH... 689s flavor: minC1|nonAB 689s Estimating DH threshold for calling LOH as the midpoint between guessed C1=0 and C1=1... 689s Argument 'midpoint': 0.5 689s Number of segments: 4 689s Number of segments in allelic balance: 1 (25.0%) of 4 689s Number of segments not in allelic balance: 2 (50.0%) of 4 689s Number of segments in allelic balance and TCN <= 3.00: 1 (25.0%) of 4 689s C: 2.07 689s Corrected C1 (=C/2): 1.03 689s Number of DHs: 777 689s Weights: 1 689s Weighted median of (corrected) C1 in allelic balance: 1.034 689s Smallest C1 among segments not in allelic balance: 0.338 689s There are 1 segments with in total 2108 heterozygous SNPs with this level. 689s Midpoint between the two: 0.686 689s Estimating DH threshold for calling LOH as the midpoint between guessed C1=0 and C1=1...done 689s delta: 0.686 689s Estimating DH threshold for calling LOH...done 689s > print(deltaLOH) 689s [1] 0.6863701 689s > ## [1] 0.625175 689s > 689s > fit <- callLOH(fit, delta=deltaLOH, verbose=-10) 689s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 689s delta (offset adjusting for bias in C1): 0.68637013 689s alpha (CI quantile; significance level): 0.05 689s Calling segments... 689s Number of segments called low C1 (LowC1, "LOH_C1"): 1 (25.00%) of 4 689s Calling segments...done 689s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 689s > print(fit) 689s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 1 1 1 1 554484 120992603 7586 1.3853 2108 689s 2 1 2 1 120992604 141510002 0 NA 0 689s 3 1 3 1 141510003 185449813 2681 2.0689 777 689s 4 1 4 1 185449813 247137334 4391 2.6341 1311 689s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean rohCall abCall lohCall 689s 1 2108 2108 0.5116 0.3382903 1.047010 FALSE FALSE TRUE 689s 2 0 NA NA NA NA NA NA NA 689s 3 777 777 0.0973 0.9337980 1.135102 FALSE TRUE FALSE 689s 4 1311 1311 0.2295 1.0147870 1.619313 FALSE FALSE FALSE 689s > plotTracks(fit) 689s > 689s > # Even if not explicitly specified, the estimated 689s > # threshold parameter is returned by the caller 689s > stopifnot(fit$params$deltaLOH == deltaLOH) 689s > 689s > 689s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 689s > # Calling segments that are gained, copy neutral, and lost 689s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 689s > fit <- callGNL(fit, verbose=-10) 689s Calling gain, neutral, and loss based TCNs of AB segments... 689s Calling neutral TCNs... 689s callCopyNeutralByTCNofAB... 689s Alpha: 0.05 689s Delta CN: 0.33085487 689s Calling copy-neutral segments... 689s Retrieve TCN confidence intervals for all segments... 689s Interval: [0.025,0.975] 689s Retrieve TCN confidence intervals for all segments...done 689s Estimating TCN confidence interval of copy-neutral AB segments... 689s calcStatsForCopyNeutralABs... 689s Identifying copy neutral AB segments... 689s Number of AB segments: 1 689s Identifying segments that are copy neutral states... 689s Number of segments in allelic balance: 1 689s Identifying segments that are copy neutral states...done 689s Number of copy-neutral AB segments: 1 689s Extracting all copy neutral AB segments across all chromosomes into one big segment... 689s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 3 1 3 1 141510003 185449813 2681 2.0689 777 689s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean rohCall abCall lohCall 689s 3 777 777 0.0973 0.933798 1.135102 FALSE TRUE FALSE 689s Extracting all copy neutral AB segments across all chromosomes into one big segment...done 689s Identifying copy neutral AB segments...done 689s Bootstrap the identified copy-neutral states... 689s Bootstrap the identified copy-neutral states...done 689s tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets dhNbrOfLoci dhMean c1Mean 689s 3 2681 2.0689 777 777 777 0.0973 0.933798 689s c2Mean tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% 689s 3 1.135102 2.055164 2.057694 2.078831 2.081454 0.08974138 0.09080508 0.1035891 689s dh_97.5% c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% 689s 3 0.1050478 0.923788 0.925412 0.9417056 0.9433752 1.124908 1.126631 1.143571 689s c2_97.5% 689s 3 1.145214 689s calcStatsForCopyNeutralABs...done 689s Bootstrap statistics for copy-neutral AB segments: 689s tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets dhNbrOfLoci dhMean c1Mean 689s 3 2681 2.0689 777 777 777 0.0973 0.933798 689s c2Mean tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% 689s 3 1.135102 2.055164 2.057694 2.078831 2.081454 0.08974138 0.09080508 0.1035891 689s dh_97.5% c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% 689s 3 0.1050478 0.923788 0.925412 0.9417056 0.9433752 1.124908 1.126631 1.143571 689s c2_97.5% 689s 3 1.145214 689s [1] "TCN statistics:" 689s tcnMean tcn_2.5% tcn_5% tcn_95% tcn_97.5% 689s 2.068900 2.055164 2.057694 2.078831 2.081454 689s 95%-confidence interval of TCN mean for the copy-neutral state: [2.05516,2.08145] (mean=2.0689) 689s Estimating TCN confidence interval of copy-neutral AB segments...done 689s Identify all copy-neutral segments... 689s DeltaCN: +/-0.330855 689s Call ("acceptance") region: [1.72431,2.41231] 689s Total number of segments: 4 689s Number of segments called allelic balance: 1 689s Number of segments called copy neutral: 1 689s Number of AB segments called copy neutral: 1 689s Number of non-AB segments called copy neutral: 0 689s Identify all copy-neutral segments...done 689s Calling copy-neutral segments...done 689s callCopyNeutralByTCNofAB...done 689s Calling neutral TCNs...done 689s Number of NTCN calls: 1 (25.00%) of 4 689s Mean TCN of AB segments: 2.06831 689s Calling loss... 689s Number of loss calls: 1 (25.00%) of 4 689s Calling loss...done 689s Calling gain... 689s Number of loss calls: 1 (25.00%) of 4 689s Calling gain...done 689s Calling gain, neutral, and loss based TCNs of AB segments...done 689s Warning message: 689s In density.default(c1, weights = weights, adjust = adjust, from = from, : 689s Selecting bandwidth *not* using 'weights' 689s > print(fit) 689s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 689s 1 1 1 1 554484 120992603 7586 1.3853 2108 689s 2 1 2 1 120992604 141510002 0 NA 0 689s 3 1 3 1 141510003 185449813 2681 2.0689 777 689s 4 1 4 1 185449813 247137334 4391 2.6341 1311 689s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean rohCall abCall lohCall 689s 1 2108 2108 0.5116 0.3382903 1.047010 FALSE FALSE TRUE 689s 2 0 NA NA NA NA NA NA NA 689s 3 777 777 0.0973 0.9337980 1.135102 FALSE TRUE FALSE 689s 4 1311 1311 0.2295 1.0147870 1.619313 FALSE FALSE FALSE 689s ntcnCall lossCall gainCall 689s 1 FALSE TRUE FALSE 689s 2 NA NA NA 689s 3 TRUE FALSE FALSE 689s 4 FALSE FALSE TRUE 689s > plotTracks(fit) 689s > 689s > proc.time() 689s user system elapsed 689s 18.222 0.852 18.930 689s Test segmentByPairedPSCBS,calls passed 689s 0 689s Begin test segmentByPairedPSCBS,futures 740s + cat segmentByPairedPSCBS,futures.Rout 740s 740s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 740s Copyright (C) 2024 The R Foundation for Statistical Computing 740s Platform: aarch64-unknown-linux-gnu (64-bit) 740s 740s R is free software and comes with ABSOLUTELY NO WARRANTY. 740s You are welcome to redistribute it under certain conditions. 740s Type 'license()' or 'licence()' for distribution details. 740s 740s R is a collaborative project with many contributors. 740s Type 'contributors()' for more information and 740s 'citation()' on how to cite R or R packages in publications. 740s 740s Type 'demo()' for some demos, 'help()' for on-line help, or 740s 'help.start()' for an HTML browser interface to help. 740s Type 'q()' to quit R. 740s 740s [Previously saved workspace restored] 740s 740s > library(PSCBS) 740s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 740s 740s Attaching package: 'PSCBS' 740s 740s The following objects are masked from 'package:base': 740s 740s append, load 740s 740s > library(utils) 740s > 740s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 740s > # Load SNP microarray data 740s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 740s > data <- PSCBS::exampleData("paired.chr01") 740s > 740s > 740s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 740s > # Paired PSCBS segmentation 740s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 740s > # Drop single-locus outliers 740s > dataS <- dropSegmentationOutliers(data) 740s > 740s > # Run light-weight tests by default 740s > if (Sys.getenv("_R_CHECK_FULL_") == "") { 740s + # Use only every 5th data point 740s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 740s + # Number of segments (for assertion) 740s + nSegs <- 4L 740s + } else { 740s + # Full tests 740s + nSegs <- 11L 740s + } 740s > 740s > str(dataS) 740s 'data.frame': 14670 obs. of 6 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 740s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 740s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 740s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 740s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 740s > 740s > 740s > ## Create multiple chromosomes 740s > data <- list() 740s > for (cc in 1:3) { 740s + dataS$chromosome <- cc 740s + data[[cc]] <- dataS 740s + } 740s > data <- Reduce(rbind, data) 740s > str(data) 740s 'data.frame': 44010 obs. of 6 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 740s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 740s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 740s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 740s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 740s > 740s > 740s > message("*** segmentByPairedPSCBS() via futures ...") 740s *** segmentByPairedPSCBS() via futures ... 740s > 740s > library("future") 740s > oplan <- plan() 740s > 740s > strategies <- c("sequential", "multisession") 740s > 740s > ## Test 'future.batchtools' futures? 740s > pkg <- "future.batchtools" 740s > if (require(pkg, character.only=TRUE)) { 740s + strategies <- c(strategies, "batchtools_local") 740s + } 740s Loading required package: future.batchtools 740s Warning message: 740s In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : 740s there is no package called 'future.batchtools' 740s > 740s > message("Future strategies to test: ", paste(sQuote(strategies), collapse=", ")) 740s Future strategies to test: 'sequential', 'multisession' 740s > 740s > fits <- list() 740s > for (strategy in strategies) { 740s + message(sprintf("- segmentByPairedPSCBS() using '%s' futures ...", strategy)) 740s + plan(strategy) 740s + fit <- segmentByPairedPSCBS(data, seed=0xBEEF, verbose=TRUE) 740s + fits[[strategy]] <- fit 740s + equal <- all.equal(fit, fits[[1]]) 740s + if (!equal) { 740s + str(fit) 740s + str(fits[[1]]) 740s + print(equal) 740s + stop(sprintf("segmentByPairedPSCBS() using '%s' futures does not produce the same results as when using '%s' futures", strategy, names(fits)[1])) 740s + } 740s + } 740s - segmentByPairedPSCBS() using 'sequential' futures ... 740s Segmenting paired tumor-normal signals using Paired PSCBS... 740s Calling genotypes from normal allele B fractions... 740s num [1:44010] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 740s Called genotypes: 740s num [1:44010] 1 0.5 0 0 0 0 1 0 1 0.5 ... 740s - attr(*, "modelFit")=List of 1 740s ..$ :List of 7 740s .. ..$ flavor : chr "density" 740s .. ..$ cn : int 2 740s .. ..$ nbrOfGenotypeGroups: int 3 740s .. ..$ tau : num [1:2] 0.312 0.678 740s .. ..$ n : int 43920 740s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 740s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 740s .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 740s .. .. ..$ density: num [1:5] 1.623 0.465 1.126 0.497 1.588 740s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 740s .. .. ..$ type : chr [1:2] "valley" "valley" 740s .. .. ..$ x : num [1:2] 0.312 0.678 740s .. .. ..$ density: num [1:2] 0.465 0.497 740s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 740s muN 740s 0 0.5 1 740s 15627 12633 15750 740s Calling genotypes from normal allele B fractions...done 740s Normalizing betaT using betaN (TumorBoost)... 740s Normalized BAFs: 740s num [1:44010] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 740s - attr(*, "modelFit")=List of 5 740s ..$ method : chr "normalizeTumorBoost" 740s ..$ flavor : chr "v4" 740s ..$ delta : num [1:44010] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 740s .. ..- attr(*, "modelFit")=List of 1 740s .. .. ..$ :List of 7 740s .. .. .. ..$ flavor : chr "density" 740s .. .. .. ..$ cn : int 2 740s .. .. .. ..$ nbrOfGenotypeGroups: int 3 740s .. .. .. ..$ tau : num [1:2] 0.312 0.678 740s .. .. .. ..$ n : int 43920 740s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 740s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 740s .. .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 740s .. .. .. .. ..$ density: num [1:5] 1.623 0.465 1.126 0.497 1.588 740s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 740s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 740s .. .. .. .. ..$ x : num [1:2] 0.312 0.678 740s .. .. .. .. ..$ density: num [1:2] 0.465 0.497 740s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 740s ..$ preserveScale: logi FALSE 740s ..$ scaleFactor : num NA 740s Normalizing betaT using betaN (TumorBoost)...done 740s Setup up data... 740s 'data.frame': 44010 obs. of 7 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 740s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 740s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 740s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 740s ..- attr(*, "modelFit")=List of 5 740s .. ..$ method : chr "normalizeTumorBoost" 740s .. ..$ flavor : chr "v4" 740s .. ..$ delta : num [1:44010] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 740s .. .. ..- attr(*, "modelFit")=List of 1 740s .. .. .. ..$ :List of 7 740s .. .. .. .. ..$ flavor : chr "density" 740s .. .. .. .. ..$ cn : int 2 740s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 740s .. .. .. .. ..$ tau : num [1:2] 0.312 0.678 740s .. .. .. .. ..$ n : int 43920 740s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 740s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 740s .. .. .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 740s .. .. .. .. .. ..$ density: num [1:5] 1.623 0.465 1.126 0.497 1.588 740s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 740s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 740s .. .. .. .. .. ..$ x : num [1:2] 0.312 0.678 740s .. .. .. .. .. ..$ density: num [1:2] 0.465 0.497 740s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 740s .. ..$ preserveScale: logi FALSE 740s .. ..$ scaleFactor : num NA 740s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 740s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 740s ..- attr(*, "modelFit")=List of 1 740s .. ..$ :List of 7 740s .. .. ..$ flavor : chr "density" 740s .. .. ..$ cn : int 2 740s .. .. ..$ nbrOfGenotypeGroups: int 3 740s .. .. ..$ tau : num [1:2] 0.312 0.678 740s .. .. ..$ n : int 43920 740s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 740s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 740s .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 740s .. .. .. ..$ density: num [1:5] 1.623 0.465 1.126 0.497 1.588 740s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 740s .. .. .. ..$ type : chr [1:2] "valley" "valley" 740s .. .. .. ..$ x : num [1:2] 0.312 0.678 740s .. .. .. ..$ density: num [1:2] 0.465 0.497 740s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 740s Setup up data...done 740s Dropping loci for which TCNs are missing... 740s Number of loci dropped: 36 740s Dropping loci for which TCNs are missing...done 740s Ordering data along genome... 740s 'data.frame': 43974 obs. of 7 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s Ordering data along genome...done 740s Segmenting multiple chromosomes... 740s Number of chromosomes: 3 740s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 740s Produced 3 seeds from this stream for future usage 740s Chromosome #1 ('Chr01') of 3... 740s 'data.frame': 14658 obs. of 8 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 740s Known segments: 740s [1] chromosome start end 740s <0 rows> (or 0-length row.names) 740s Segmenting paired tumor-normal signals using Paired PSCBS... 740s Setup up data... 740s 'data.frame': 14658 obs. of 7 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s Setup up data...done 740s Ordering data along genome... 740s 'data.frame': 14658 obs. of 7 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s Ordering data along genome...done 740s Keeping only current chromosome for 'knownSegments'... 740s Chromosome: 1 740s Known segments for this chromosome: 740s [1] chromosome start end 740s <0 rows> (or 0-length row.names) 740s Keeping only current chromosome for 'knownSegments'...done 740s alphaTCN: 0.009 740s alphaDH: 0.001 740s Number of loci: 14658 740s Calculating DHs... 740s Number of SNPs: 14658 740s Number of heterozygous SNPs: 4209 (28.71%) 740s Normalized DHs: 740s num [1:14658] NA NA NA NA NA ... 740s Calculating DHs...done 740s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 740s Produced 2 seeds from this stream for future usage 740s Identification of change points by total copy numbers... 740s Segmenting by CBS... 740s Chromosome: 1 740s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 14658 obs. of 4 variables: 740s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 740s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 740s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 3 obs. of 6 variables: 740s ..$ sampleName: chr [1:3] NA NA NA 740s ..$ chromosome: int [1:3] 1 1 1 740s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 740s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 740s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 740s ..$ mean : num [1:3] 1.39 2.07 2.63 740s $ segRows:'data.frame': 3 obs. of 2 variables: 740s ..$ startRow: int [1:3] 1 7600 10268 740s ..$ endRow : int [1:3] 7599 10267 14658 740s $ params :List of 5 740s ..$ alpha : num 0.009 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 1 740s .. ..$ start : num -Inf 740s .. ..$ end : num Inf 740s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 1.4 0 1.4 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s Identification of change points by total copy numbers...done 740s Restructure TCN segmentation results... 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 740s 1 1 554484 143926517 7599 1.3859 740s 2 1 143926517 185449813 2668 2.0704 740s 3 1 185449813 247137334 4391 2.6341 740s Number of TCN segments: 3 740s Restructure TCN segmentation results...done 740s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 740s Number of TCN loci in segment: 7599 740s Locus data for TCN segment: 740s 'data.frame': 7599 obs. of 9 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 740s $ rho : num NA NA NA NA NA ... 740s Number of loci: 7599 740s Number of SNPs: 2120 (27.90%) 740s Number of heterozygous SNPs: 2120 (100.00%) 740s Chromosome: 1 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 1 740s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 7599 obs. of 4 variables: 740s ..$ chromosome: int [1:7599] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 740s ..$ y : num [1:7599] NA NA NA NA NA ... 740s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 1 740s ..$ start : num 554484 740s ..$ end : num 1.44e+08 740s ..$ nbrOfLoci : int 2120 740s ..$ mean : num 0.51 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 10 740s ..$ endRow : int 7594 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 1 740s .. ..$ start : num 554484 740s .. ..$ end : num 1.44e+08 740s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.081 0 0.081 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 10 7594 740s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 10 7594 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 554484 143926517 2120 0.5101 740s startRow endRow 740s 1 10 7594 740s Rows: 740s [1] 1 740s TCN segmentation rows: 740s startRow endRow 740s 1 1 7599 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s startRow endRow 740s 1 10 7594 740s NULL 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s startRow endRow 740s 1 1 7599 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 1 1 554484 143926517 7599 1.3859 2120 2120 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 143926517 7599 1.3859 2120 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 1 2120 554484 143926517 2120 0.5101 740s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 740s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 740s Number of TCN loci in segment: 2668 740s Locus data for TCN segment: 740s 'data.frame': 2668 obs. of 9 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 740s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 740s $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 740s $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 740s $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... 740s $ muN : num 0 1 1 0 0 1 0 0 0 0 ... 740s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 740s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 740s Number of loci: 2668 740s Number of SNPs: 775 (29.05%) 740s Number of heterozygous SNPs: 775 (100.00%) 740s Chromosome: 1 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 1 740s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 2668 obs. of 4 variables: 740s ..$ chromosome: int [1:2668] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 740s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 740s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 1 740s ..$ start : num 1.44e+08 740s ..$ end : num 1.85e+08 740s ..$ nbrOfLoci : int 775 740s ..$ mean : num 0.097 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 15 740s ..$ endRow : int 2664 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 1 740s .. ..$ start : num 1.44e+08 740s .. ..$ end : num 1.85e+08 740s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.032 0 0.033 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 15 2664 740s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 7614 10263 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 143926517 185449813 775 0.097 740s startRow endRow 740s 1 7614 10263 740s Rows: 740s [1] 2 740s TCN segmentation rows: 740s startRow endRow 740s 2 7600 10267 740s TCN and DH segmentation rows: 740s startRow endRow 740s 2 7600 10267 740s startRow endRow 740s 1 7614 10263 740s startRow endRow 740s 1 1 7599 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s 2 7614 10263 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 2 1 143926517 185449813 2668 2.0704 775 775 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 2 2 1 1 143926517 185449813 2668 2.0704 775 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 2 775 143926517 185449813 775 0.097 740s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 740s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 740s Number of TCN loci in segment: 4391 740s Locus data for TCN segment: 740s 'data.frame': 4391 obs. of 9 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 740s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 740s $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... 740s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 740s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 740s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 740s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 740s $ rho : num NA 0.2186 NA 0.0503 NA ... 740s Number of loci: 4391 740s Number of SNPs: 1314 (29.92%) 740s Number of heterozygous SNPs: 1314 (100.00%) 740s Chromosome: 1 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 1 740s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 4391 obs. of 4 variables: 740s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 740s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 740s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 1 740s ..$ start : num 1.85e+08 740s ..$ end : num 2.47e+08 740s ..$ nbrOfLoci : int 1314 740s ..$ mean : num 0.23 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 2 740s ..$ endRow : int 4388 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 1 740s .. ..$ start : num 1.85e+08 740s .. ..$ end : num 2.47e+08 740s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.048 0 0.048 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 2 4388 740s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 10269 14655 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 185449813 247137334 1314 0.2295 740s startRow endRow 740s 1 10269 14655 740s Rows: 740s [1] 3 740s TCN segmentation rows: 740s startRow endRow 740s 3 10268 14658 740s TCN and DH segmentation rows: 740s startRow endRow 740s 3 10268 14658 740s startRow endRow 740s 1 10269 14655 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s 2 7614 10263 740s 3 10269 14655 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 3 1 185449813 247137334 4391 2.6341 1314 1314 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 3 3 1 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 3 1314 185449813 247137334 1314 0.2295 740s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 143926517 7599 1.3859 2120 740s 2 1 2 1 143926517 185449813 2668 2.0704 775 740s 3 1 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 1 2120 554484 143926517 2120 0.5101 740s 2 775 143926517 185449813 775 0.0970 740s 3 1314 185449813 247137334 1314 0.2295 740s Calculating (C1,C2) per segment... 740s Calculating (C1,C2) per segment...done 740s Number of segments: 3 740s Segmenting paired tumor-normal signals using Paired PSCBS...done 740s Post-segmenting TCNs... 740s Number of segments: 3 740s Number of chromosomes: 1 740s [1] 1 740s Chromosome 1 ('chr01') of 1... 740s Rows: 740s [1] 1 2 3 740s Number of segments: 3 740s TCN segment #1 ('1') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #1 ('1') of 3...done 740s TCN segment #2 ('2') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #2 ('2') of 3...done 740s TCN segment #3 ('3') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #3 ('3') of 3...done 740s Chromosome 1 ('chr01') of 1...done 740s Update (C1,C2) per segment... 740s Update (C1,C2) per segment...done 740s Post-segmenting TCNs...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 143926517 7599 1.3859 2120 740s 2 1 2 1 143926517 185449813 2668 2.0704 775 740s 3 1 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 143926517 7599 1.3859 2120 740s 2 1 2 1 143926517 185449813 2668 2.0704 775 740s 3 1 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 143926517 7599 1.3859 2120 740s 2 1 2 1 143926517 185449813 2668 2.0704 775 740s 3 1 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 143926517 7599 1.3859 2120 740s 2 1 2 1 143926517 185449813 2668 2.0704 775 740s 3 1 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s Chromosome #1 ('Chr01') of 3...done 740s Chromosome #2 ('Chr02') of 3... 740s 'data.frame': 14658 obs. of 8 variables: 740s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s $ index : int 14659 14660 14661 14662 14663 14664 14665 14666 14667 14668 ... 740s Known segments: 740s [1] chromosome start end 740s <0 rows> (or 0-length row.names) 740s Segmenting paired tumor-normal signals using Paired PSCBS... 740s Setup up data... 740s 'data.frame': 14658 obs. of 7 variables: 740s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s Setup up data...done 740s Ordering data along genome... 740s 'data.frame': 14658 obs. of 7 variables: 740s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s Ordering data along genome...done 740s Keeping only current chromosome for 'knownSegments'... 740s Chromosome: 2 740s Known segments for this chromosome: 740s [1] chromosome start end 740s <0 rows> (or 0-length row.names) 740s Keeping only current chromosome for 'knownSegments'...done 740s alphaTCN: 0.009 740s alphaDH: 0.001 740s Number of loci: 14658 740s Calculating DHs... 740s Number of SNPs: 14658 740s Number of heterozygous SNPs: 4209 (28.71%) 740s Normalized DHs: 740s num [1:14658] NA NA NA NA NA ... 740s Calculating DHs...done 740s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 740s Produced 2 seeds from this stream for future usage 740s Identification of change points by total copy numbers... 740s Segmenting by CBS... 740s Chromosome: 2 740s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 14658 obs. of 4 variables: 740s ..$ chromosome: int [1:14658] 2 2 2 2 2 2 2 2 2 2 ... 740s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 740s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 740s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 3 obs. of 6 variables: 740s ..$ sampleName: chr [1:3] NA NA NA 740s ..$ chromosome: int [1:3] 2 2 2 740s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 740s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 740s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 740s ..$ mean : num [1:3] 1.39 2.07 2.63 740s $ segRows:'data.frame': 3 obs. of 2 variables: 740s ..$ startRow: int [1:3] 1 7600 10268 740s ..$ endRow : int [1:3] 7599 10267 14658 740s $ params :List of 5 740s ..$ alpha : num 0.009 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 2 740s .. ..$ start : num -Inf 740s .. ..$ end : num Inf 740s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 1.66 0 1.66 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 740s Identification of change points by total copy numbers...done 740s Restructure TCN segmentation results... 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 740s 1 2 554484 143926517 7599 1.3859 740s 2 2 143926517 185449813 2668 2.0704 740s 3 2 185449813 247137334 4391 2.6341 740s Number of TCN segments: 3 740s Restructure TCN segmentation results...done 740s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 740s Number of TCN loci in segment: 7599 740s Locus data for TCN segment: 740s 'data.frame': 7599 obs. of 9 variables: 740s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 740s $ rho : num NA NA NA NA NA ... 740s Number of loci: 7599 740s Number of SNPs: 2120 (27.90%) 740s Number of heterozygous SNPs: 2120 (100.00%) 740s Chromosome: 2 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 2 740s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 7599 obs. of 4 variables: 740s ..$ chromosome: int [1:7599] 2 2 2 2 2 2 2 2 2 2 ... 740s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 740s ..$ y : num [1:7599] NA NA NA NA NA ... 740s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 2 740s ..$ start : num 554484 740s ..$ end : num 1.44e+08 740s ..$ nbrOfLoci : int 2120 740s ..$ mean : num 0.51 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 10 740s ..$ endRow : int 7594 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 2 740s .. ..$ start : num 554484 740s .. ..$ end : num 1.44e+08 740s ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.082 0 0.082 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 10 7594 740s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 10 7594 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 554484 143926517 2120 0.5101 740s startRow endRow 740s 1 10 7594 740s Rows: 740s [1] 1 740s TCN segmentation rows: 740s startRow endRow 740s 1 1 7599 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s startRow endRow 740s 1 10 7594 740s NULL 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s startRow endRow 740s 1 1 7599 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 1 2 554484 143926517 7599 1.3859 2120 2120 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 2 554484 143926517 7599 1.3859 2120 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 1 2120 554484 143926517 2120 0.5101 740s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 740s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 740s Number of TCN loci in segment: 2668 740s Locus data for TCN segment: 740s 'data.frame': 2668 obs. of 9 variables: 740s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 740s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 740s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 740s $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 740s $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 740s $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... 740s $ muN : num 0 1 1 0 0 1 0 0 0 0 ... 740s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 740s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 740s Number of loci: 2668 740s Number of SNPs: 775 (29.05%) 740s Number of heterozygous SNPs: 775 (100.00%) 740s Chromosome: 2 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 2 740s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 2668 obs. of 4 variables: 740s ..$ chromosome: int [1:2668] 2 2 2 2 2 2 2 2 2 2 ... 740s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 740s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 740s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 2 740s ..$ start : num 1.44e+08 740s ..$ end : num 1.85e+08 740s ..$ nbrOfLoci : int 775 740s ..$ mean : num 0.097 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 15 740s ..$ endRow : int 2664 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 2 740s .. ..$ start : num 1.44e+08 740s .. ..$ end : num 1.85e+08 740s ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.067 0.001 0.068 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 15 2664 740s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 7614 10263 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 143926517 185449813 775 0.097 740s startRow endRow 740s 1 7614 10263 740s Rows: 740s [1] 2 740s TCN segmentation rows: 740s startRow endRow 740s 2 7600 10267 740s TCN and DH segmentation rows: 740s startRow endRow 740s 2 7600 10267 740s startRow endRow 740s 1 7614 10263 740s startRow endRow 740s 1 1 7599 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s 2 7614 10263 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 2 2 143926517 185449813 2668 2.0704 775 775 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 2 2 1 2 143926517 185449813 2668 2.0704 775 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 2 775 143926517 185449813 775 0.097 740s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 740s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 740s Number of TCN loci in segment: 4391 740s Locus data for TCN segment: 740s 'data.frame': 4391 obs. of 9 variables: 740s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 740s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 740s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 740s $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... 740s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 740s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 740s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 740s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 740s $ rho : num NA 0.2186 NA 0.0503 NA ... 740s Number of loci: 4391 740s Number of SNPs: 1314 (29.92%) 740s Number of heterozygous SNPs: 1314 (100.00%) 740s Chromosome: 2 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 2 740s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 4391 obs. of 4 variables: 740s ..$ chromosome: int [1:4391] 2 2 2 2 2 2 2 2 2 2 ... 740s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 740s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 740s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 2 740s ..$ start : num 1.85e+08 740s ..$ end : num 2.47e+08 740s ..$ nbrOfLoci : int 1314 740s ..$ mean : num 0.23 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 2 740s ..$ endRow : int 4388 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 2 740s .. ..$ start : num 1.85e+08 740s .. ..$ end : num 2.47e+08 740s ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.051 0 0.051 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 2 4388 740s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 10269 14655 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 185449813 247137334 1314 0.2295 740s startRow endRow 740s 1 10269 14655 740s Rows: 740s [1] 3 740s TCN segmentation rows: 740s startRow endRow 740s 3 10268 14658 740s TCN and DH segmentation rows: 740s startRow endRow 740s 3 10268 14658 740s startRow endRow 740s 1 10269 14655 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s 2 7614 10263 740s 3 10269 14655 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 3 2 185449813 247137334 4391 2.6341 1314 1314 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 3 3 1 2 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 3 1314 185449813 247137334 1314 0.2295 740s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 2 1 1 554484 143926517 7599 1.3859 2120 740s 2 2 2 1 143926517 185449813 2668 2.0704 775 740s 3 2 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 1 2120 554484 143926517 2120 0.5101 740s 2 775 143926517 185449813 775 0.0970 740s 3 1314 185449813 247137334 1314 0.2295 740s Calculating (C1,C2) per segment... 740s Calculating (C1,C2) per segment...done 740s Number of segments: 3 740s Segmenting paired tumor-normal signals using Paired PSCBS...done 740s Post-segmenting TCNs... 740s Number of segments: 3 740s Number of chromosomes: 1 740s [1] 2 740s Chromosome 1 ('chr02') of 1... 740s Rows: 740s [1] 1 2 3 740s Number of segments: 3 740s TCN segment #1 ('1') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #1 ('1') of 3...done 740s TCN segment #2 ('2') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #2 ('2') of 3...done 740s TCN segment #3 ('3') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #3 ('3') of 3...done 740s Chromosome 1 ('chr02') of 1...done 740s Update (C1,C2) per segment... 740s Update (C1,C2) per segment...done 740s Post-segmenting TCNs...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 2 1 1 554484 143926517 7599 1.3859 2120 740s 2 2 2 1 143926517 185449813 2668 2.0704 775 740s 3 2 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 2 1 1 554484 143926517 7599 1.3859 2120 740s 2 2 2 1 143926517 185449813 2668 2.0704 775 740s 3 2 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 2 1 1 554484 143926517 7599 1.3859 2120 740s 2 2 2 1 143926517 185449813 2668 2.0704 775 740s 3 2 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 2 1 1 554484 143926517 7599 1.3859 2120 740s 2 2 2 1 143926517 185449813 2668 2.0704 775 740s 3 2 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s Chromosome #2 ('Chr02') of 3...done 740s Chromosome #3 ('Chr03') of 3... 740s 'data.frame': 14658 obs. of 8 variables: 740s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s $ index : int 29317 29318 29319 29320 29321 29322 29323 29324 29325 29326 ... 740s Known segments: 740s [1] chromosome start end 740s <0 rows> (or 0-length row.names) 740s Segmenting paired tumor-normal signals using Paired PSCBS... 740s Setup up data... 740s 'data.frame': 14658 obs. of 7 variables: 740s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s Setup up data...done 740s Ordering data along genome... 740s 'data.frame': 14658 obs. of 7 variables: 740s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s Ordering data along genome...done 740s Keeping only current chromosome for 'knownSegments'... 740s Chromosome: 3 740s Known segments for this chromosome: 740s [1] chromosome start end 740s <0 rows> (or 0-length row.names) 740s Keeping only current chromosome for 'knownSegments'...done 740s alphaTCN: 0.009 740s alphaDH: 0.001 740s Number of loci: 14658 740s Calculating DHs... 740s Number of SNPs: 14658 740s Number of heterozygous SNPs: 4209 (28.71%) 740s Normalized DHs: 740s num [1:14658] NA NA NA NA NA ... 740s Calculating DHs...done 740s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 740s Produced 2 seeds from this stream for future usage 740s Identification of change points by total copy numbers... 740s Segmenting by CBS... 740s Chromosome: 3 740s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 14658 obs. of 4 variables: 740s ..$ chromosome: int [1:14658] 3 3 3 3 3 3 3 3 3 3 ... 740s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 740s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 740s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 3 obs. of 6 variables: 740s ..$ sampleName: chr [1:3] NA NA NA 740s ..$ chromosome: int [1:3] 3 3 3 740s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 740s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 740s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 740s ..$ mean : num [1:3] 1.39 2.07 2.63 740s $ segRows:'data.frame': 3 obs. of 2 variables: 740s ..$ startRow: int [1:3] 1 7600 10268 740s ..$ endRow : int [1:3] 7599 10267 14658 740s $ params :List of 5 740s ..$ alpha : num 0.009 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 3 740s .. ..$ start : num -Inf 740s .. ..$ end : num Inf 740s ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 1.36 0 1.36 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 740s Identification of change points by total copy numbers...done 740s Restructure TCN segmentation results... 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 740s 1 3 554484 143926517 7599 1.3859 740s 2 3 143926517 185449813 2668 2.0704 740s 3 3 185449813 247137334 4391 2.6341 740s Number of TCN segments: 3 740s Restructure TCN segmentation results...done 740s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 740s Number of TCN loci in segment: 7599 740s Locus data for TCN segment: 740s 'data.frame': 7599 obs. of 9 variables: 740s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 740s $ rho : num NA NA NA NA NA ... 740s Number of loci: 7599 740s Number of SNPs: 2120 (27.90%) 740s Number of heterozygous SNPs: 2120 (100.00%) 740s Chromosome: 3 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 3 740s Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 7599 obs. of 4 variables: 740s ..$ chromosome: int [1:7599] 3 3 3 3 3 3 3 3 3 3 ... 740s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 740s ..$ y : num [1:7599] NA NA NA NA NA ... 740s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 3 740s ..$ start : num 554484 740s ..$ end : num 1.44e+08 740s ..$ nbrOfLoci : int 2120 740s ..$ mean : num 0.51 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 10 740s ..$ endRow : int 7594 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 3 740s .. ..$ start : num 554484 740s .. ..$ end : num 1.44e+08 740s ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.097 0 0.097 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 10 7594 740s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 10 7594 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 554484 143926517 2120 0.5101 740s startRow endRow 740s 1 10 7594 740s Rows: 740s [1] 1 740s TCN segmentation rows: 740s startRow endRow 740s 1 1 7599 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s startRow endRow 740s 1 10 7594 740s NULL 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s startRow endRow 740s 1 1 7599 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 1 3 554484 143926517 7599 1.3859 2120 2120 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 3 554484 143926517 7599 1.3859 2120 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 1 2120 554484 143926517 2120 0.5101 740s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 740s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 740s Number of TCN loci in segment: 2668 740s Locus data for TCN segment: 740s 'data.frame': 2668 obs. of 9 variables: 740s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 740s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 740s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 740s $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 740s $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 740s $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... 740s $ muN : num 0 1 1 0 0 1 0 0 0 0 ... 740s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 740s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 740s Number of loci: 2668 740s Number of SNPs: 775 (29.05%) 740s Number of heterozygous SNPs: 775 (100.00%) 740s Chromosome: 3 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 3 740s Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 2668 obs. of 4 variables: 740s ..$ chromosome: int [1:2668] 3 3 3 3 3 3 3 3 3 3 ... 740s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 740s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 740s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 3 740s ..$ start : num 1.44e+08 740s ..$ end : num 1.85e+08 740s ..$ nbrOfLoci : int 775 740s ..$ mean : num 0.097 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 15 740s ..$ endRow : int 2664 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 3 740s .. ..$ start : num 1.44e+08 740s .. ..$ end : num 1.85e+08 740s ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.027 0 0.027 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 15 2664 740s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 7614 10263 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 143926517 185449813 775 0.097 740s startRow endRow 740s 1 7614 10263 740s Rows: 740s [1] 2 740s TCN segmentation rows: 740s startRow endRow 740s 2 7600 10267 740s TCN and DH segmentation rows: 740s startRow endRow 740s 2 7600 10267 740s startRow endRow 740s 1 7614 10263 740s startRow endRow 740s 1 1 7599 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s 2 7614 10263 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 2 3 143926517 185449813 2668 2.0704 775 775 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 2 2 1 3 143926517 185449813 2668 2.0704 775 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 2 775 143926517 185449813 775 0.097 740s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 740s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 740s Number of TCN loci in segment: 4391 740s Locus data for TCN segment: 740s 'data.frame': 4391 obs. of 9 variables: 740s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 740s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 740s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 740s $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... 740s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 740s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 740s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 740s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 740s $ rho : num NA 0.2186 NA 0.0503 NA ... 740s Number of loci: 4391 740s Number of SNPs: 1314 (29.92%) 740s Number of heterozygous SNPs: 1314 (100.00%) 740s Chromosome: 3 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 3 740s Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 4391 obs. of 4 variables: 740s ..$ chromosome: int [1:4391] 3 3 3 3 3 3 3 3 3 3 ... 740s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 740s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 740s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 3 740s ..$ start : num 1.85e+08 740s ..$ end : num 2.47e+08 740s ..$ nbrOfLoci : int 1314 740s ..$ mean : num 0.23 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 2 740s ..$ endRow : int 4388 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 3 740s .. ..$ start : num 1.85e+08 740s .. ..$ end : num 2.47e+08 740s ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.048 0 0.048 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 2 4388 740s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 10269 14655 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 185449813 247137334 1314 0.2295 740s startRow endRow 740s 1 10269 14655 740s Rows: 740s [1] 3 740s TCN segmentation rows: 740s startRow endRow 740s 3 10268 14658 740s TCN and DH segmentation rows: 740s startRow endRow 740s 3 10268 14658 740s startRow endRow 740s 1 10269 14655 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s 2 7614 10263 740s 3 10269 14655 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 3 3 185449813 247137334 4391 2.6341 1314 1314 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 3 3 1 3 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 3 1314 185449813 247137334 1314 0.2295 740s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 3 1 1 554484 143926517 7599 1.3859 2120 740s 2 3 2 1 143926517 185449813 2668 2.0704 775 740s 3 3 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 1 2120 554484 143926517 2120 0.5101 740s 2 775 143926517 185449813 775 0.0970 740s 3 1314 185449813 247137334 1314 0.2295 740s Calculating (C1,C2) per segment... 740s Calculating (C1,C2) per segment...done 740s Number of segments: 3 740s Segmenting paired tumor-normal signals using Paired PSCBS...done 740s Post-segmenting TCNs... 740s Number of segments: 3 740s Number of chromosomes: 1 740s [1] 3 740s Chromosome 1 ('chr03') of 1... 740s Rows: 740s [1] 1 2 3 740s Number of segments: 3 740s TCN segment #1 ('1') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #1 ('1') of 3...done 740s TCN segment #2 ('2') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #2 ('2') of 3...done 740s TCN segment #3 ('3') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #3 ('3') of 3...done 740s Chromosome 1 ('chr03') of 1...done 740s Update (C1,C2) per segment... 740s Update (C1,C2) per segment...done 740s Post-segmenting TCNs...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 3 1 1 554484 143926517 7599 1.3859 2120 740s 2 3 2 1 143926517 185449813 2668 2.0704 775 740s 3 3 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 3 1 1 554484 143926517 7599 1.3859 2120 740s 2 3 2 1 143926517 185449813 2668 2.0704 775 740s 3 3 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 3 1 1 554484 143926517 7599 1.3859 2120 740s 2 3 2 1 143926517 185449813 2668 2.0704 775 740s 3 3 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 3 1 1 554484 143926517 7599 1.3859 2120 740s 2 3 2 1 143926517 185449813 2668 2.0704 775 740s 3 3 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s Chromosome #3 ('Chr03') of 3...done 740s Merging (independently) segmented chromosome... 740s List of 5 740s $ data :Classes 'PairedPSCNData' and 'data.frame': 43974 obs. of 8 variables: 740s ..$ chromosome: int [1:43974] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:43974] 554484 730720 782343 878522 916294 ... 740s ..$ CT : num [1:43974] 1.88 1.8 1.59 1.64 1.53 ... 740s ..$ betaT : num [1:43974] 0.0646 0.1672 0.9284 0.113 0.7209 ... 740s ..$ betaTN : num [1:43974] -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s ..$ betaN : num [1:43974] 0.116 0.284 0.909 0.082 0.86 ... 740s ..$ muN : num [1:43974] 0 0 1 0 1 1 1 0 1 0.5 ... 740s ..$ rho : num [1:43974] NA NA NA NA NA ... 740s $ output :Classes 'PairedPSCNSegments' and 'data.frame': 11 obs. of 15 variables: 740s ..$ chromosome : int [1:11] 1 1 1 NA 2 2 2 NA 3 3 ... 740s ..$ tcnId : int [1:11] 1 2 3 NA 1 2 3 NA 1 2 ... 740s ..$ dhId : int [1:11] 1 1 1 NA 1 1 1 NA 1 1 ... 740s ..$ tcnStart : num [1:11] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... 740s ..$ tcnEnd : num [1:11] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... 740s ..$ tcnNbrOfLoci: int [1:11] 7599 2668 4391 NA 7599 2668 4391 NA 7599 2668 ... 740s ..$ tcnMean : num [1:11] 1.39 2.07 2.63 NA 1.39 ... 740s ..$ tcnNbrOfSNPs: int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... 740s ..$ tcnNbrOfHets: int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... 740s ..$ dhStart : num [1:11] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... 740s ..$ dhEnd : num [1:11] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... 740s ..$ dhNbrOfLoci : int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... 740s ..$ dhMean : num [1:11] 0.51 0.097 0.23 NA 0.51 ... 740s ..$ c1Mean : num [1:11] 0.339 0.935 1.015 NA 0.339 ... 740s ..$ c2Mean : num [1:11] 1.05 1.14 1.62 NA 1.05 ... 740s $ tcnSegRows:'data.frame': 11 obs. of 2 variables: 740s ..$ startRow: int [1:11] 1 7600 10268 NA 14659 22258 24926 NA 29317 36916 ... 740s ..$ endRow : int [1:11] 7599 10267 14658 NA 22257 24925 29316 NA 36915 39583 ... 740s $ dhSegRows :'data.frame': 11 obs. of 2 variables: 740s ..$ startRow: int [1:11] 10 7614 10269 NA 14668 22272 24927 NA 29326 36930 ... 740s ..$ endRow : int [1:11] 7594 10263 14655 NA 22252 24921 29313 NA 36910 39579 ... 740s $ params :List of 7 740s ..$ alphaTCN : num 0.009 740s ..$ alphaDH : num 0.001 740s ..$ flavor : chr "tcn&dh" 740s ..$ tbn : logi FALSE 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 0 obs. of 3 variables: 740s .. ..$ chromosome: int(0) 740s .. ..$ start : int(0) 740s .. ..$ end : int(0) 740s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 740s - attr(*, "class")= chr [1:3] "PairedPSCBS" "PSCBS" "AbstractCBS" 740s Merging (independently) segmented chromosome...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 143926517 7599 1.3859 2120 740s 2 1 2 1 143926517 185449813 2668 2.0704 775 740s 3 1 3 1 185449813 247137334 4391 2.6341 1314 740s 4 NA NA NA NA NA NA NA NA 740s 5 2 1 1 554484 143926517 7599 1.3859 2120 740s 6 2 2 1 143926517 185449813 2668 2.0704 775 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s 4 NA NA NA NA NA NA NA 740s 5 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 6 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 6 2 2 1 143926517 185449813 2668 2.0704 775 740s 7 2 3 1 185449813 247137334 4391 2.6341 1314 740s 8 NA NA NA NA NA NA NA NA 740s 9 3 1 1 554484 143926517 7599 1.3859 2120 740s 10 3 2 1 143926517 185449813 2668 2.0704 775 740s 11 3 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 6 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 7 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s 8 NA NA NA NA NA NA NA 740s 9 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 10 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 11 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s Segmenting multiple chromosomes...done 740s Segmenting paired tumor-normal signals using Paired PSCBS...done 740s - segmentByPairedPSCBS() using 'multisession' futures ... 740s Segmenting paired tumor-normal signals using Paired PSCBS... 740s Calling genotypes from normal allele B fractions... 740s num [1:44010] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 740s Called genotypes: 740s num [1:44010] 1 0.5 0 0 0 0 1 0 1 0.5 ... 740s - attr(*, "modelFit")=List of 1 740s ..$ :List of 7 740s .. ..$ flavor : chr "density" 740s .. ..$ cn : int 2 740s .. ..$ nbrOfGenotypeGroups: int 3 740s .. ..$ tau : num [1:2] 0.312 0.678 740s .. ..$ n : int 43920 740s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 740s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 740s .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 740s .. .. ..$ density: num [1:5] 1.623 0.465 1.126 0.497 1.588 740s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 740s .. .. ..$ type : chr [1:2] "valley" "valley" 740s .. .. ..$ x : num [1:2] 0.312 0.678 740s .. .. ..$ density: num [1:2] 0.465 0.497 740s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 740s muN 740s 0 0.5 1 740s 15627 12633 15750 740s Calling genotypes from normal allele B fractions...done 740s Normalizing betaT using betaN (TumorBoost)... 740s Normalized BAFs: 740s num [1:44010] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 740s - attr(*, "modelFit")=List of 5 740s ..$ method : chr "normalizeTumorBoost" 740s ..$ flavor : chr "v4" 740s ..$ delta : num [1:44010] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 740s .. ..- attr(*, "modelFit")=List of 1 740s .. .. ..$ :List of 7 740s .. .. .. ..$ flavor : chr "density" 740s .. .. .. ..$ cn : int 2 740s .. .. .. ..$ nbrOfGenotypeGroups: int 3 740s .. .. .. ..$ tau : num [1:2] 0.312 0.678 740s .. .. .. ..$ n : int 43920 740s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 740s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 740s .. .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 740s .. .. .. .. ..$ density: num [1:5] 1.623 0.465 1.126 0.497 1.588 740s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 740s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 740s .. .. .. .. ..$ x : num [1:2] 0.312 0.678 740s .. .. .. .. ..$ density: num [1:2] 0.465 0.497 740s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 740s ..$ preserveScale: logi FALSE 740s ..$ scaleFactor : num NA 740s Normalizing betaT using betaN (TumorBoost)...done 740s Setup up data... 740s 'data.frame': 44010 obs. of 7 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 740s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 740s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 740s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 740s ..- attr(*, "modelFit")=List of 5 740s .. ..$ method : chr "normalizeTumorBoost" 740s .. ..$ flavor : chr "v4" 740s .. ..$ delta : num [1:44010] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 740s .. .. ..- attr(*, "modelFit")=List of 1 740s .. .. .. ..$ :List of 7 740s .. .. .. .. ..$ flavor : chr "density" 740s .. .. .. .. ..$ cn : int 2 740s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 740s .. .. .. .. ..$ tau : num [1:2] 0.312 0.678 740s .. .. .. .. ..$ n : int 43920 740s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 740s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 740s .. .. .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 740s .. .. .. .. .. ..$ density: num [1:5] 1.623 0.465 1.126 0.497 1.588 740s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 740s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 740s .. .. .. .. .. ..$ x : num [1:2] 0.312 0.678 740s .. .. .. .. .. ..$ density: num [1:2] 0.465 0.497 740s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 740s .. ..$ preserveScale: logi FALSE 740s .. ..$ scaleFactor : num NA 740s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 740s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 740s ..- attr(*, "modelFit")=List of 1 740s .. ..$ :List of 7 740s .. .. ..$ flavor : chr "density" 740s .. .. ..$ cn : int 2 740s .. .. ..$ nbrOfGenotypeGroups: int 3 740s .. .. ..$ tau : num [1:2] 0.312 0.678 740s .. .. ..$ n : int 43920 740s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 740s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 740s .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 740s .. .. .. ..$ density: num [1:5] 1.623 0.465 1.126 0.497 1.588 740s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 740s .. .. .. ..$ type : chr [1:2] "valley" "valley" 740s .. .. .. ..$ x : num [1:2] 0.312 0.678 740s .. .. .. ..$ density: num [1:2] 0.465 0.497 740s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 740s Setup up data...done 740s Dropping loci for which TCNs are missing... 740s Number of loci dropped: 36 740s Dropping loci for which TCNs are missing...done 740s Ordering data along genome... 740s 'data.frame': 43974 obs. of 7 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s Ordering data along genome...done 740s Segmenting multiple chromosomes... 740s Number of chromosomes: 3 740s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 740s Produced 3 seeds from this stream for future usage 740s Chromosome #1 ('Chr01') of 3... 740s 'data.frame': 14658 obs. of 8 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 740s Known segments: 740s [1] chromosome start end 740s <0 rows> (or 0-length row.names) 740s Segmenting paired tumor-normal signals using Paired PSCBS... 740s Setup up data... 740s 'data.frame': 14658 obs. of 7 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s Setup up data...done 740s Ordering data along genome... 740s 'data.frame': 14658 obs. of 7 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s Ordering data along genome...done 740s Keeping only current chromosome for 'knownSegments'... 740s Chromosome: 1 740s Known segments for this chromosome: 740s [1] chromosome start end 740s <0 rows> (or 0-length row.names) 740s Keeping only current chromosome for 'knownSegments'...done 740s alphaTCN: 0.009 740s alphaDH: 0.001 740s Number of loci: 14658 740s Calculating DHs... 740s Number of SNPs: 14658 740s Number of heterozygous SNPs: 4209 (28.71%) 740s Normalized DHs: 740s num [1:14658] NA NA NA NA NA ... 740s Calculating DHs...done 740s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 740s Produced 2 seeds from this stream for future usage 740s Identification of change points by total copy numbers... 740s Segmenting by CBS... 740s Chromosome: 1 740s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 14658 obs. of 4 variables: 740s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 740s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 740s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 3 obs. of 6 variables: 740s ..$ sampleName: chr [1:3] NA NA NA 740s ..$ chromosome: int [1:3] 1 1 1 740s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 740s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 740s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 740s ..$ mean : num [1:3] 1.39 2.07 2.63 740s $ segRows:'data.frame': 3 obs. of 2 variables: 740s ..$ startRow: int [1:3] 1 7600 10268 740s ..$ endRow : int [1:3] 7599 10267 14658 740s $ params :List of 5 740s ..$ alpha : num 0.009 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 1 740s .. ..$ start : num -Inf 740s .. ..$ end : num Inf 740s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 1.33 0 1.33 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s Identification of change points by total copy numbers...done 740s Restructure TCN segmentation results... 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 740s 1 1 554484 143926517 7599 1.3859 740s 2 1 143926517 185449813 2668 2.0704 740s 3 1 185449813 247137334 4391 2.6341 740s Number of TCN segments: 3 740s Restructure TCN segmentation results...done 740s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 740s Number of TCN loci in segment: 7599 740s Locus data for TCN segment: 740s 'data.frame': 7599 obs. of 9 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 740s $ rho : num NA NA NA NA NA ... 740s Number of loci: 7599 740s Number of SNPs: 2120 (27.90%) 740s Number of heterozygous SNPs: 2120 (100.00%) 740s Chromosome: 1 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 1 740s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 7599 obs. of 4 variables: 740s ..$ chromosome: int [1:7599] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 740s ..$ y : num [1:7599] NA NA NA NA NA ... 740s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 1 740s ..$ start : num 554484 740s ..$ end : num 1.44e+08 740s ..$ nbrOfLoci : int 2120 740s ..$ mean : num 0.51 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 10 740s ..$ endRow : int 7594 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 1 740s .. ..$ start : num 554484 740s .. ..$ end : num 1.44e+08 740s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.101 0 0.101 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 10 7594 740s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 10 7594 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 554484 143926517 2120 0.5101 740s startRow endRow 740s 1 10 7594 740s Rows: 740s [1] 1 740s TCN segmentation rows: 740s startRow endRow 740s 1 1 7599 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s startRow endRow 740s 1 10 7594 740s NULL 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s startRow endRow 740s 1 1 7599 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 1 1 554484 143926517 7599 1.3859 2120 2120 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 143926517 7599 1.3859 2120 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 1 2120 554484 143926517 2120 0.5101 740s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 740s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 740s Number of TCN loci in segment: 2668 740s Locus data for TCN segment: 740s 'data.frame': 2668 obs. of 9 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 740s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 740s $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 740s $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 740s $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... 740s $ muN : num 0 1 1 0 0 1 0 0 0 0 ... 740s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 740s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 740s Number of loci: 2668 740s Number of SNPs: 775 (29.05%) 740s Number of heterozygous SNPs: 775 (100.00%) 740s Chromosome: 1 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 1 740s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 2668 obs. of 4 variables: 740s ..$ chromosome: int [1:2668] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 740s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 740s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 1 740s ..$ start : num 1.44e+08 740s ..$ end : num 1.85e+08 740s ..$ nbrOfLoci : int 775 740s ..$ mean : num 0.097 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 15 740s ..$ endRow : int 2664 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 1 740s .. ..$ start : num 1.44e+08 740s .. ..$ end : num 1.85e+08 740s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.041 0 0.042 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 15 2664 740s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 7614 10263 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 143926517 185449813 775 0.097 740s startRow endRow 740s 1 7614 10263 740s Rows: 740s [1] 2 740s TCN segmentation rows: 740s startRow endRow 740s 2 7600 10267 740s TCN and DH segmentation rows: 740s startRow endRow 740s 2 7600 10267 740s startRow endRow 740s 1 7614 10263 740s startRow endRow 740s 1 1 7599 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s 2 7614 10263 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 2 1 143926517 185449813 2668 2.0704 775 775 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 2 2 1 1 143926517 185449813 2668 2.0704 775 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 2 775 143926517 185449813 775 0.097 740s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 740s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 740s Number of TCN loci in segment: 4391 740s Locus data for TCN segment: 740s 'data.frame': 4391 obs. of 9 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 740s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 740s $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... 740s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 740s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 740s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 740s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 740s $ rho : num NA 0.2186 NA 0.0503 NA ... 740s Number of loci: 4391 740s Number of SNPs: 1314 (29.92%) 740s Number of heterozygous SNPs: 1314 (100.00%) 740s Chromosome: 1 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 1 740s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 4391 obs. of 4 variables: 740s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 740s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 740s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 1 740s ..$ start : num 1.85e+08 740s ..$ end : num 2.47e+08 740s ..$ nbrOfLoci : int 1314 740s ..$ mean : num 0.23 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 2 740s ..$ endRow : int 4388 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 1 740s .. ..$ start : num 1.85e+08 740s .. ..$ end : num 2.47e+08 740s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.049 0 0.049 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 2 4388 740s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 10269 14655 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 185449813 247137334 1314 0.2295 740s startRow endRow 740s 1 10269 14655 740s Rows: 740s [1] 3 740s TCN segmentation rows: 740s startRow endRow 740s 3 10268 14658 740s TCN and DH segmentation rows: 740s startRow endRow 740s 3 10268 14658 740s startRow endRow 740s 1 10269 14655 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s 2 7614 10263 740s 3 10269 14655 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 3 1 185449813 247137334 4391 2.6341 1314 1314 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 3 3 1 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 3 1314 185449813 247137334 1314 0.2295 740s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 143926517 7599 1.3859 2120 740s 2 1 2 1 143926517 185449813 2668 2.0704 775 740s 3 1 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 1 2120 554484 143926517 2120 0.5101 740s 2 775 143926517 185449813 775 0.0970 740s 3 1314 185449813 247137334 1314 0.2295 740s Calculating (C1,C2) per segment... 740s Calculating (C1,C2) per segment...done 740s Number of segments: 3 740s Segmenting paired tumor-normal signals using Paired PSCBS...done 740s Post-segmenting TCNs... 740s Number of segments: 3 740s Number of chromosomes: 1 740s [1] 1 740s Chromosome 1 ('chr01') of 1... 740s Rows: 740s [1] 1 2 3 740s Number of segments: 3 740s TCN segment #1 ('1') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #1 ('1') of 3...done 740s TCN segment #2 ('2') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #2 ('2') of 3...done 740s TCN segment #3 ('3') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #3 ('3') of 3...done 740s Chromosome 1 ('chr01') of 1...done 740s Update (C1,C2) per segment... 740s Update (C1,C2) per segment...done 740s Post-segmenting TCNs...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 143926517 7599 1.3859 2120 740s 2 1 2 1 143926517 185449813 2668 2.0704 775 740s 3 1 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 143926517 7599 1.3859 2120 740s 2 1 2 1 143926517 185449813 2668 2.0704 775 740s 3 1 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 143926517 7599 1.3859 2120 740s 2 1 2 1 143926517 185449813 2668 2.0704 775 740s 3 1 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 143926517 7599 1.3859 2120 740s 2 1 2 1 143926517 185449813 2668 2.0704 775 740s 3 1 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s Chromosome #1 ('Chr01') of 3...done 740s Chromosome #2 ('Chr02') of 3... 740s 'data.frame': 14658 obs. of 8 variables: 740s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s $ index : int 14659 14660 14661 14662 14663 14664 14665 14666 14667 14668 ... 740s Known segments: 740s [1] chromosome start end 740s <0 rows> (or 0-length row.names) 740s Segmenting paired tumor-normal signals using Paired PSCBS... 740s Setup up data... 740s 'data.frame': 14658 obs. of 7 variables: 740s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s Setup up data...done 740s Ordering data along genome... 740s 'data.frame': 14658 obs. of 7 variables: 740s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s Ordering data along genome...done 740s Keeping only current chromosome for 'knownSegments'... 740s Chromosome: 2 740s Known segments for this chromosome: 740s [1] chromosome start end 740s <0 rows> (or 0-length row.names) 740s Keeping only current chromosome for 'knownSegments'...done 740s alphaTCN: 0.009 740s alphaDH: 0.001 740s Number of loci: 14658 740s Calculating DHs... 740s Number of SNPs: 14658 740s Number of heterozygous SNPs: 4209 (28.71%) 740s Normalized DHs: 740s num [1:14658] NA NA NA NA NA ... 740s Calculating DHs...done 740s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 740s Produced 2 seeds from this stream for future usage 740s Identification of change points by total copy numbers... 740s Segmenting by CBS... 740s Chromosome: 2 740s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 14658 obs. of 4 variables: 740s ..$ chromosome: int [1:14658] 2 2 2 2 2 2 2 2 2 2 ... 740s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 740s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 740s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 3 obs. of 6 variables: 740s ..$ sampleName: chr [1:3] NA NA NA 740s ..$ chromosome: int [1:3] 2 2 2 740s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 740s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 740s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 740s ..$ mean : num [1:3] 1.39 2.07 2.63 740s $ segRows:'data.frame': 3 obs. of 2 variables: 740s ..$ startRow: int [1:3] 1 7600 10268 740s ..$ endRow : int [1:3] 7599 10267 14658 740s $ params :List of 5 740s ..$ alpha : num 0.009 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 2 740s .. ..$ start : num -Inf 740s .. ..$ end : num Inf 740s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 1.54 0 1.54 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 740s Identification of change points by total copy numbers...done 740s Restructure TCN segmentation results... 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 740s 1 2 554484 143926517 7599 1.3859 740s 2 2 143926517 185449813 2668 2.0704 740s 3 2 185449813 247137334 4391 2.6341 740s Number of TCN segments: 3 740s Restructure TCN segmentation results...done 740s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 740s Number of TCN loci in segment: 7599 740s Locus data for TCN segment: 740s 'data.frame': 7599 obs. of 9 variables: 740s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 740s $ rho : num NA NA NA NA NA ... 740s Number of loci: 7599 740s Number of SNPs: 2120 (27.90%) 740s Number of heterozygous SNPs: 2120 (100.00%) 740s Chromosome: 2 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 2 740s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 7599 obs. of 4 variables: 740s ..$ chromosome: int [1:7599] 2 2 2 2 2 2 2 2 2 2 ... 740s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 740s ..$ y : num [1:7599] NA NA NA NA NA ... 740s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 2 740s ..$ start : num 554484 740s ..$ end : num 1.44e+08 740s ..$ nbrOfLoci : int 2120 740s ..$ mean : num 0.51 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 10 740s ..$ endRow : int 7594 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 2 740s .. ..$ start : num 554484 740s .. ..$ end : num 1.44e+08 740s ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.104 0.001 0.105 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 10 7594 740s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 10 7594 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 554484 143926517 2120 0.5101 740s startRow endRow 740s 1 10 7594 740s Rows: 740s [1] 1 740s TCN segmentation rows: 740s startRow endRow 740s 1 1 7599 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s startRow endRow 740s 1 10 7594 740s NULL 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s startRow endRow 740s 1 1 7599 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 1 2 554484 143926517 7599 1.3859 2120 2120 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 2 554484 143926517 7599 1.3859 2120 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 1 2120 554484 143926517 2120 0.5101 740s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 740s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 740s Number of TCN loci in segment: 2668 740s Locus data for TCN segment: 740s 'data.frame': 2668 obs. of 9 variables: 740s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 740s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 740s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 740s $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 740s $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 740s $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... 740s $ muN : num 0 1 1 0 0 1 0 0 0 0 ... 740s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 740s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 740s Number of loci: 2668 740s Number of SNPs: 775 (29.05%) 740s Number of heterozygous SNPs: 775 (100.00%) 740s Chromosome: 2 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 2 740s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 2668 obs. of 4 variables: 740s ..$ chromosome: int [1:2668] 2 2 2 2 2 2 2 2 2 2 ... 740s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 740s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 740s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 2 740s ..$ start : num 1.44e+08 740s ..$ end : num 1.85e+08 740s ..$ nbrOfLoci : int 775 740s ..$ mean : num 0.097 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 15 740s ..$ endRow : int 2664 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 2 740s .. ..$ start : num 1.44e+08 740s .. ..$ end : num 1.85e+08 740s ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.028 0 0.028 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 15 2664 740s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 7614 10263 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 143926517 185449813 775 0.097 740s startRow endRow 740s 1 7614 10263 740s Rows: 740s [1] 2 740s TCN segmentation rows: 740s startRow endRow 740s 2 7600 10267 740s TCN and DH segmentation rows: 740s startRow endRow 740s 2 7600 10267 740s startRow endRow 740s 1 7614 10263 740s startRow endRow 740s 1 1 7599 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s 2 7614 10263 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 2 2 143926517 185449813 2668 2.0704 775 775 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 2 2 1 2 143926517 185449813 2668 2.0704 775 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 2 775 143926517 185449813 775 0.097 740s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 740s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 740s Number of TCN loci in segment: 4391 740s Locus data for TCN segment: 740s 'data.frame': 4391 obs. of 9 variables: 740s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 740s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 740s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 740s $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... 740s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 740s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 740s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 740s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 740s $ rho : num NA 0.2186 NA 0.0503 NA ... 740s Number of loci: 4391 740s Number of SNPs: 1314 (29.92%) 740s Number of heterozygous SNPs: 1314 (100.00%) 740s Chromosome: 2 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 2 740s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 4391 obs. of 4 variables: 740s ..$ chromosome: int [1:4391] 2 2 2 2 2 2 2 2 2 2 ... 740s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 740s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 740s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 2 740s ..$ start : num 1.85e+08 740s ..$ end : num 2.47e+08 740s ..$ nbrOfLoci : int 1314 740s ..$ mean : num 0.23 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 2 740s ..$ endRow : int 4388 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 2 740s .. ..$ start : num 1.85e+08 740s .. ..$ end : num 2.47e+08 740s ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.048 0 0.048 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 2 4388 740s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 10269 14655 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 185449813 247137334 1314 0.2295 740s startRow endRow 740s 1 10269 14655 740s Rows: 740s [1] 3 740s TCN segmentation rows: 740s startRow endRow 740s 3 10268 14658 740s TCN and DH segmentation rows: 740s startRow endRow 740s 3 10268 14658 740s startRow endRow 740s 1 10269 14655 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s 2 7614 10263 740s 3 10269 14655 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 3 2 185449813 247137334 4391 2.6341 1314 1314 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 3 3 1 2 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 3 1314 185449813 247137334 1314 0.2295 740s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 2 1 1 554484 143926517 7599 1.3859 2120 740s 2 2 2 1 143926517 185449813 2668 2.0704 775 740s 3 2 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 1 2120 554484 143926517 2120 0.5101 740s 2 775 143926517 185449813 775 0.0970 740s 3 1314 185449813 247137334 1314 0.2295 740s Calculating (C1,C2) per segment... 740s Calculating (C1,C2) per segment...done 740s Number of segments: 3 740s Segmenting paired tumor-normal signals using Paired PSCBS...done 740s Post-segmenting TCNs... 740s Number of segments: 3 740s Number of chromosomes: 1 740s [1] 2 740s Chromosome 1 ('chr02') of 1... 740s Rows: 740s [1] 1 2 3 740s Number of segments: 3 740s TCN segment #1 ('1') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #1 ('1') of 3...done 740s TCN segment #2 ('2') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #2 ('2') of 3...done 740s TCN segment #3 ('3') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #3 ('3') of 3...done 740s Chromosome 1 ('chr02') of 1...done 740s Update (C1,C2) per segment... 740s Update (C1,C2) per segment...done 740s Post-segmenting TCNs...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 2 1 1 554484 143926517 7599 1.3859 2120 740s 2 2 2 1 143926517 185449813 2668 2.0704 775 740s 3 2 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 2 1 1 554484 143926517 7599 1.3859 2120 740s 2 2 2 1 143926517 185449813 2668 2.0704 775 740s 3 2 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 2 1 1 554484 143926517 7599 1.3859 2120 740s 2 2 2 1 143926517 185449813 2668 2.0704 775 740s 3 2 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 2 1 1 554484 143926517 7599 1.3859 2120 740s 2 2 2 1 143926517 185449813 2668 2.0704 775 740s 3 2 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s Chromosome #2 ('Chr02') of 3...done 740s Chromosome #3 ('Chr03') of 3... 740s 'data.frame': 14658 obs. of 8 variables: 740s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s $ index : int 29317 29318 29319 29320 29321 29322 29323 29324 29325 29326 ... 740s Known segments: 740s [1] chromosome start end 740s <0 rows> (or 0-length row.names) 740s Segmenting paired tumor-normal signals using Paired PSCBS... 740s Setup up data... 740s 'data.frame': 14658 obs. of 7 variables: 740s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s Setup up data...done 740s Ordering data along genome... 740s 'data.frame': 14658 obs. of 7 variables: 740s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s Ordering data along genome...done 740s Keeping only current chromosome for 'knownSegments'... 740s Chromosome: 3 740s Known segments for this chromosome: 740s [1] chromosome start end 740s <0 rows> (or 0-length row.names) 740s Keeping only current chromosome for 'knownSegments'...done 740s alphaTCN: 0.009 740s alphaDH: 0.001 740s Number of loci: 14658 740s Calculating DHs... 740s Number of SNPs: 14658 740s Number of heterozygous SNPs: 4209 (28.71%) 740s Normalized DHs: 740s num [1:14658] NA NA NA NA NA ... 740s Calculating DHs...done 740s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 740s Produced 2 seeds from this stream for future usage 740s Identification of change points by total copy numbers... 740s Segmenting by CBS... 740s Chromosome: 3 740s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 14658 obs. of 4 variables: 740s ..$ chromosome: int [1:14658] 3 3 3 3 3 3 3 3 3 3 ... 740s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 740s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 740s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 3 obs. of 6 variables: 740s ..$ sampleName: chr [1:3] NA NA NA 740s ..$ chromosome: int [1:3] 3 3 3 740s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 740s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 740s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 740s ..$ mean : num [1:3] 1.39 2.07 2.63 740s $ segRows:'data.frame': 3 obs. of 2 variables: 740s ..$ startRow: int [1:3] 1 7600 10268 740s ..$ endRow : int [1:3] 7599 10267 14658 740s $ params :List of 5 740s ..$ alpha : num 0.009 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 3 740s .. ..$ start : num -Inf 740s .. ..$ end : num Inf 740s ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 1.72 0 1.73 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 740s Identification of change points by total copy numbers...done 740s Restructure TCN segmentation results... 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 740s 1 3 554484 143926517 7599 1.3859 740s 2 3 143926517 185449813 2668 2.0704 740s 3 3 185449813 247137334 4391 2.6341 740s Number of TCN segments: 3 740s Restructure TCN segmentation results...done 740s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 740s Number of TCN loci in segment: 7599 740s Locus data for TCN segment: 740s 'data.frame': 7599 obs. of 9 variables: 740s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 740s $ rho : num NA NA NA NA NA ... 740s Number of loci: 7599 740s Number of SNPs: 2120 (27.90%) 740s Number of heterozygous SNPs: 2120 (100.00%) 740s Chromosome: 3 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 3 740s Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 7599 obs. of 4 variables: 740s ..$ chromosome: int [1:7599] 3 3 3 3 3 3 3 3 3 3 ... 740s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 740s ..$ y : num [1:7599] NA NA NA NA NA ... 740s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 3 740s ..$ start : num 554484 740s ..$ end : num 1.44e+08 740s ..$ nbrOfLoci : int 2120 740s ..$ mean : num 0.51 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 10 740s ..$ endRow : int 7594 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 3 740s .. ..$ start : num 554484 740s .. ..$ end : num 1.44e+08 740s ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.092 0 0.092 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 10 7594 740s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 10 7594 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 554484 143926517 2120 0.5101 740s startRow endRow 740s 1 10 7594 740s Rows: 740s [1] 1 740s TCN segmentation rows: 740s startRow endRow 740s 1 1 7599 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s startRow endRow 740s 1 10 7594 740s NULL 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s startRow endRow 740s 1 1 7599 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 1 3 554484 143926517 7599 1.3859 2120 2120 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 3 554484 143926517 7599 1.3859 2120 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 1 2120 554484 143926517 2120 0.5101 740s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 740s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 740s Number of TCN loci in segment: 2668 740s Locus data for TCN segment: 740s 'data.frame': 2668 obs. of 9 variables: 740s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 740s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 740s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 740s $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 740s $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 740s $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... 740s $ muN : num 0 1 1 0 0 1 0 0 0 0 ... 740s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 740s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 740s Number of loci: 2668 740s Number of SNPs: 775 (29.05%) 740s Number of heterozygous SNPs: 775 (100.00%) 740s Chromosome: 3 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 3 740s Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 2668 obs. of 4 variables: 740s ..$ chromosome: int [1:2668] 3 3 3 3 3 3 3 3 3 3 ... 740s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 740s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 740s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 3 740s ..$ start : num 1.44e+08 740s ..$ end : num 1.85e+08 740s ..$ nbrOfLoci : int 775 740s ..$ mean : num 0.097 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 15 740s ..$ endRow : int 2664 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 3 740s .. ..$ start : num 1.44e+08 740s .. ..$ end : num 1.85e+08 740s ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.039 0 0.039 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 15 2664 740s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 7614 10263 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 143926517 185449813 775 0.097 740s startRow endRow 740s 1 7614 10263 740s Rows: 740s [1] 2 740s TCN segmentation rows: 740s startRow endRow 740s 2 7600 10267 740s TCN and DH segmentation rows: 740s startRow endRow 740s 2 7600 10267 740s startRow endRow 740s 1 7614 10263 740s startRow endRow 740s 1 1 7599 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s 2 7614 10263 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 2 3 143926517 185449813 2668 2.0704 775 775 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 2 2 1 3 143926517 185449813 2668 2.0704 775 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 2 775 143926517 185449813 775 0.097 740s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 740s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 740s Number of TCN loci in segment: 4391 740s Locus data for TCN segment: 740s 'data.frame': 4391 obs. of 9 variables: 740s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 740s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 740s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 740s $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... 740s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 740s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 740s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 740s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 740s $ rho : num NA 0.2186 NA 0.0503 NA ... 740s Number of loci: 4391 740s Number of SNPs: 1314 (29.92%) 740s Number of heterozygous SNPs: 1314 (100.00%) 740s Chromosome: 3 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 3 740s Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 4391 obs. of 4 variables: 740s ..$ chromosome: int [1:4391] 3 3 3 3 3 3 3 3 3 3 ... 740s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 740s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 740s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 3 740s ..$ start : num 1.85e+08 740s ..$ end : num 2.47e+08 740s ..$ nbrOfLoci : int 1314 740s ..$ mean : num 0.23 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 2 740s ..$ endRow : int 4388 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 3 740s .. ..$ start : num 1.85e+08 740s .. ..$ end : num 2.47e+08 740s ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.052 0 0.052 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 2 4388 740s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 10269 14655 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 185449813 247137334 1314 0.2295 740s startRow endRow 740s 1 10269 14655 740s Rows: 740s [1] 3 740s TCN segmentation rows: 740s startRow endRow 740s 3 10268 14658 740s TCN and DH segmentation rows: 740s startRow endRow 740s 3 10268 14658 740s startRow endRow 740s 1 10269 14655 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s startRow endRow 740s 1 10 7594 740s 2 7614 10263 740s 3 10269 14655 740s startRow endRow 740s 1 1 7599 740s 2 7600 10267 740s 3 10268 14658 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 3 3 185449813 247137334 4391 2.6341 1314 1314 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 3 3 1 3 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 3 1314 185449813 247137334 1314 0.2295 740s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 3 1 1 554484 143926517 7599 1.3859 2120 740s 2 3 2 1 143926517 185449813 2668 2.0704 775 740s 3 3 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 1 2120 554484 143926517 2120 0.5101 740s 2 775 143926517 185449813 775 0.0970 740s 3 1314 185449813 247137334 1314 0.2295 740s Calculating (C1,C2) per segment... 740s Calculating (C1,C2) per segment...done 740s Number of segments: 3 740s Segmenting paired tumor-normal signals using Paired PSCBS...done 740s Post-segmenting TCNs... 740s Number of segments: 3 740s Number of chromosomes: 1 740s [1] 3 740s Chromosome 1 ('chr03') of 1... 740s Rows: 740s [1] 1 2 3 740s Number of segments: 3 740s TCN segment #1 ('1') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #1 ('1') of 3...done 740s TCN segment #2 ('2') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #2 ('2') of 3...done 740s TCN segment #3 ('3') of 3... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #3 ('3') of 3...done 740s Chromosome 1 ('chr03') of 1...done 740s Update (C1,C2) per segment... 740s Update (C1,C2) per segment...done 740s Post-segmenting TCNs...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 3 1 1 554484 143926517 7599 1.3859 2120 740s 2 3 2 1 143926517 185449813 2668 2.0704 775 740s 3 3 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 3 1 1 554484 143926517 7599 1.3859 2120 740s 2 3 2 1 143926517 185449813 2668 2.0704 775 740s 3 3 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 3 1 1 554484 143926517 7599 1.3859 2120 740s 2 3 2 1 143926517 185449813 2668 2.0704 775 740s 3 3 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 3 1 1 554484 143926517 7599 1.3859 2120 740s 2 3 2 1 143926517 185449813 2668 2.0704 775 740s 3 3 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s Chromosome #3 ('Chr03') of 3...done 740s Merging (independently) segmented chromosome... 740s List of 5 740s $ data :Classes 'PairedPSCNData' and 'data.frame': 43974 obs. of 8 variables: 740s ..$ chromosome: int [1:43974] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:43974] 554484 730720 782343 878522 916294 ... 740s ..$ CT : num [1:43974] 1.88 1.8 1.59 1.64 1.53 ... 740s ..$ betaT : num [1:43974] 0.0646 0.1672 0.9284 0.113 0.7209 ... 740s ..$ betaTN : num [1:43974] -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s ..$ betaN : num [1:43974] 0.116 0.284 0.909 0.082 0.86 ... 740s ..$ muN : num [1:43974] 0 0 1 0 1 1 1 0 1 0.5 ... 740s ..$ rho : num [1:43974] NA NA NA NA NA ... 740s $ output :Classes 'PairedPSCNSegments' and 'data.frame': 11 obs. of 15 variables: 740s ..$ chromosome : int [1:11] 1 1 1 NA 2 2 2 NA 3 3 ... 740s ..$ tcnId : int [1:11] 1 2 3 NA 1 2 3 NA 1 2 ... 740s ..$ dhId : int [1:11] 1 1 1 NA 1 1 1 NA 1 1 ... 740s ..$ tcnStart : num [1:11] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... 740s ..$ tcnEnd : num [1:11] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... 740s ..$ tcnNbrOfLoci: int [1:11] 7599 2668 4391 NA 7599 2668 4391 NA 7599 2668 ... 740s ..$ tcnMean : num [1:11] 1.39 2.07 2.63 NA 1.39 ... 740s ..$ tcnNbrOfSNPs: int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... 740s ..$ tcnNbrOfHets: int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... 740s ..$ dhStart : num [1:11] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... 740s ..$ dhEnd : num [1:11] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... 740s ..$ dhNbrOfLoci : int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... 740s ..$ dhMean : num [1:11] 0.51 0.097 0.23 NA 0.51 ... 740s ..$ c1Mean : num [1:11] 0.339 0.935 1.015 NA 0.339 ... 740s ..$ c2Mean : num [1:11] 1.05 1.14 1.62 NA 1.05 ... 740s $ tcnSegRows:'data.frame': 11 obs. of 2 variables: 740s ..$ startRow: int [1:11] 1 7600 10268 NA 14659 22258 24926 NA 29317 36916 ... 740s ..$ endRow : int [1:11] 7599 10267 14658 NA 22257 24925 29316 NA 36915 39583 ... 740s $ dhSegRows :'data.frame': 11 obs. of 2 variables: 740s ..$ startRow: int [1:11] 10 7614 10269 NA 14668 22272 24927 NA 29326 36930 ... 740s ..$ endRow : int [1:11] 7594 10263 14655 NA 22252 24921 29313 NA 36910 39579 ... 740s $ params :List of 7 740s ..$ alphaTCN : num 0.009 740s ..$ alphaDH : num 0.001 740s ..$ flavor : chr "tcn&dh" 740s ..$ tbn : logi FALSE 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 0 obs. of 3 variables: 740s .. ..$ chromosome: int(0) 740s .. ..$ start : int(0) 740s .. ..$ end : int(0) 740s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 740s - attr(*, "class")= chr [1:3] "PairedPSCBS" "PSCBS" "AbstractCBS" 740s Merging (independently) segmented chromosome...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 143926517 7599 1.3859 2120 740s 2 1 2 1 143926517 185449813 2668 2.0704 775 740s 3 1 3 1 185449813 247137334 4391 2.6341 1314 740s 4 NA NA NA NA NA NA NA NA 740s 5 2 1 1 554484 143926517 7599 1.3859 2120 740s 6 2 2 1 143926517 185449813 2668 2.0704 775 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s 4 NA NA NA NA NA NA NA 740s 5 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 6 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 6 2 2 1 143926517 185449813 2668 2.0704 775 740s 7 2 3 1 185449813 247137334 4391 2.6341 1314 740s 8 NA NA NA NA NA NA NA NA 740s 9 3 1 1 554484 143926517 7599 1.3859 2120 740s 10 3 2 1 143926517 185449813 2668 2.0704 775 740s 11 3 3 1 185449813 247137334 4391 2.6341 1314 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 6 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 7 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s 8 NA NA NA NA NA NA NA 740s 9 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 740s 10 775 143926517 185449813 775 0.0970 0.9347856 1.135614 740s 11 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 740s Segmenting multiple chromosomes...done 740s Segmenting paired tumor-normal signals using Paired PSCBS...done 740s > 740s > message("*** segmentByPairedPSCBS() via futures ... DONE") 740s *** segmentByPairedPSCBS() via futures ... DONE 740s > 740s > 740s > message("*** segmentByPairedPSCBS() via futures with known segments ...") 740s *** segmentByPairedPSCBS() via futures with known segments ... 740s > fits <- list() 740s > dataT <- subset(data, chromosome == 1) 740s > gaps <- findLargeGaps(dataT, minLength=2e6) 740s > knownSegments <- gapsToSegments(gaps) 740s > 740s > for (strategy in strategies) { 740s + message(sprintf("- segmentByPairedPSCBS() w/ known segments using '%s' futures ...", strategy)) 740s + plan(strategy) 740s + fit <- segmentByPairedPSCBS(dataT, knownSegments=knownSegments, seed=0xBEEF, verbose=TRUE) 740s + fits[[strategy]] <- fit 740s + equal <- all.equal(fit, fits[[1]]) 740s + if (!equal) { 740s + str(fit) 740s + str(fits[[1]]) 740s + print(equal) 740s + stop(sprintf("segmentByPairedPSCBS() w/ known segments using '%s' futures does not produce the same results as when using '%s' futures", strategy, names(fits)[1])) 740s + } 740s + } 740s - segmentByPairedPSCBS() w/ known segments using 'sequential' futures ... 740s Segmenting paired tumor-normal signals using Paired PSCBS... 740s Calling genotypes from normal allele B fractions... 740s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 740s Called genotypes: 740s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 740s - attr(*, "modelFit")=List of 1 740s ..$ :List of 7 740s .. ..$ flavor : chr "density" 740s .. ..$ cn : int 2 740s .. ..$ nbrOfGenotypeGroups: int 3 740s .. ..$ tau : num [1:2] 0.315 0.677 740s .. ..$ n : int 14640 740s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 740s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 740s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 740s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 740s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 740s .. .. ..$ type : chr [1:2] "valley" "valley" 740s .. .. ..$ x : num [1:2] 0.315 0.677 740s .. .. ..$ density: num [1:2] 0.522 0.552 740s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 740s muN 740s 0 0.5 1 740s 5221 4198 5251 740s Calling genotypes from normal allele B fractions...done 740s Normalizing betaT using betaN (TumorBoost)... 740s Normalized BAFs: 740s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 740s - attr(*, "modelFit")=List of 5 740s ..$ method : chr "normalizeTumorBoost" 740s ..$ flavor : chr "v4" 740s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 740s .. ..- attr(*, "modelFit")=List of 1 740s .. .. ..$ :List of 7 740s .. .. .. ..$ flavor : chr "density" 740s .. .. .. ..$ cn : int 2 740s .. .. .. ..$ nbrOfGenotypeGroups: int 3 740s .. .. .. ..$ tau : num [1:2] 0.315 0.677 740s .. .. .. ..$ n : int 14640 740s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 740s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 740s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 740s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 740s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 740s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 740s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 740s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 740s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 740s ..$ preserveScale: logi FALSE 740s ..$ scaleFactor : num NA 740s Normalizing betaT using betaN (TumorBoost)...done 740s Setup up data... 740s 'data.frame': 14670 obs. of 7 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 740s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 740s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 740s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 740s ..- attr(*, "modelFit")=List of 5 740s .. ..$ method : chr "normalizeTumorBoost" 740s .. ..$ flavor : chr "v4" 740s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 740s .. .. ..- attr(*, "modelFit")=List of 1 740s .. .. .. ..$ :List of 7 740s .. .. .. .. ..$ flavor : chr "density" 740s .. .. .. .. ..$ cn : int 2 740s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 740s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 740s .. .. .. .. ..$ n : int 14640 740s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 740s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 740s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 740s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 740s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 740s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 740s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 740s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 740s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 740s .. ..$ preserveScale: logi FALSE 740s .. ..$ scaleFactor : num NA 740s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 740s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 740s ..- attr(*, "modelFit")=List of 1 740s .. ..$ :List of 7 740s .. .. ..$ flavor : chr "density" 740s .. .. ..$ cn : int 2 740s .. .. ..$ nbrOfGenotypeGroups: int 3 740s .. .. ..$ tau : num [1:2] 0.315 0.677 740s .. .. ..$ n : int 14640 740s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 740s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 740s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 740s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 740s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 740s .. .. .. ..$ type : chr [1:2] "valley" "valley" 740s .. .. .. ..$ x : num [1:2] 0.315 0.677 740s .. .. .. ..$ density: num [1:2] 0.522 0.552 740s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 740s Setup up data...done 740s Dropping loci for which TCNs are missing... 740s Number of loci dropped: 12 740s Dropping loci for which TCNs are missing...done 740s Ordering data along genome... 740s 'data.frame': 14658 obs. of 7 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s Ordering data along genome...done 740s Keeping only current chromosome for 'knownSegments'... 740s Chromosome: 1 740s Known segments for this chromosome: 740s chromosome start end length 740s 1 1 -Inf 120908858 Inf 740s 2 1 120908859 142693887 21785028 740s 3 1 142693888 Inf Inf 740s Keeping only current chromosome for 'knownSegments'...done 740s alphaTCN: 0.009 740s alphaDH: 0.001 740s Number of loci: 14658 740s Calculating DHs... 740s Number of SNPs: 14658 740s Number of heterozygous SNPs: 4196 (28.63%) 740s Normalized DHs: 740s num [1:14658] NA NA NA NA NA ... 740s Calculating DHs...done 740s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 740s Produced 2 seeds from this stream for future usage 740s Identification of change points by total copy numbers... 740s Segmenting by CBS... 740s Chromosome: 1 740s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 740s Produced 3 seeds from this stream for future usage 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 14658 obs. of 4 variables: 740s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 740s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 740s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 4 obs. of 6 variables: 740s ..$ sampleName: chr [1:4] NA NA NA NA 740s ..$ chromosome: int [1:4] 1 1 1 1 740s ..$ start : num [1:4] 5.54e+05 1.21e+08 1.43e+08 1.85e+08 740s ..$ end : num [1:4] 1.21e+08 1.43e+08 1.85e+08 2.47e+08 740s ..$ nbrOfLoci : int [1:4] 7586 0 2681 4391 740s ..$ mean : num [1:4] 1.39 NA 2.07 2.63 740s $ segRows:'data.frame': 4 obs. of 2 variables: 740s ..$ startRow: int [1:4] 1 NA 7587 10268 740s ..$ endRow : int [1:4] 7586 NA 10267 14658 740s $ params :List of 5 740s ..$ alpha : num 0.009 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 4 obs. of 3 variables: 740s .. ..$ chromosome: int [1:4] 1 1 2 1 740s .. ..$ start : num [1:4] -Inf -Inf -Inf 1.43e+08 740s .. ..$ end : num [1:4] 1.21e+08 Inf Inf Inf 740s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.493 0 0.494 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s Identification of change points by total copy numbers...done 740s Restructure TCN segmentation results... 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 740s 1 1 554484 120908858 7586 1.3853 740s 2 1 120908859 142693887 0 NA 740s 3 1 142693888 185449813 2681 2.0689 740s 4 1 185449813 247137334 4391 2.6341 740s Number of TCN segments: 4 740s Restructure TCN segmentation results...done 740s Total CN segment #1 ([ 554484,1.20909e+08]) of 4... 740s Number of TCN loci in segment: 7586 740s Locus data for TCN segment: 740s 'data.frame': 7586 obs. of 9 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 740s $ rho : num NA NA NA NA NA ... 740s Number of loci: 7586 740s Number of SNPs: 2108 (27.79%) 740s Number of heterozygous SNPs: 2108 (100.00%) 740s Chromosome: 1 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 1 740s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 7586 obs. of 4 variables: 740s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 740s ..$ y : num [1:7586] NA NA NA NA NA ... 740s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 1 740s ..$ start : num 554484 740s ..$ end : num 1.21e+08 740s ..$ nbrOfLoci : int 2108 740s ..$ mean : num 0.512 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 10 740s ..$ endRow : int 7574 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 1 740s .. ..$ start : num 554484 740s .. ..$ end : num 1.21e+08 740s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.163 0 0.163 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 10 7574 740s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 10 7574 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 554484 120908858 2108 0.5116 740s startRow endRow 740s 1 10 7574 740s Rows: 740s [1] 1 740s TCN segmentation rows: 740s startRow endRow 740s 1 1 7586 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7586 740s startRow endRow 740s 1 10 7574 740s NULL 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7586 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s 4 10268 14658 740s startRow endRow 740s 1 10 7574 740s startRow endRow 740s 1 1 7586 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 1 1 554484 120908858 7586 1.3853 2108 2108 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 120908858 7586 1.3853 2108 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 1 2108 554484 120908858 2108 0.5116 740s Total CN segment #1 ([ 554484,1.20909e+08]) of 4...done 740s Total CN segment #2 ([1.20909e+08,1.42694e+08]) of 4... 740s Number of TCN loci in segment: 0 740s Locus data for TCN segment: 740s 'data.frame': 0 obs. of 9 variables: 740s $ chromosome: int 740s $ x : num 740s $ CT : num 740s $ betaT : num 740s $ betaTN : num 740s $ betaN : num 740s $ muN : num 740s $ index : int 740s $ rho : num 740s Number of loci: 0 740s Number of SNPs: 0 (NaN%) 740s Number of heterozygous SNPs: 0 (NaN%) 740s Chromosome: 1 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: NA 740s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 0 obs. of 4 variables: 740s ..$ chromosome: int(0) 740s ..$ x : num(0) 740s ..$ y : num(0) 740s ..$ index : int(0) 740s $ output :'data.frame': 0 obs. of 6 variables: 740s ..$ sampleName: chr(0) 740s ..$ chromosome: num(0) 740s ..$ start : num(0) 740s ..$ end : num(0) 740s ..$ nbrOfLoci : int(0) 740s ..$ mean : num(0) 740s $ segRows:'data.frame': 0 obs. of 2 variables: 740s ..$ startRow: int(0) 740s ..$ endRow : int(0) 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 0 obs. of 3 variables: 740s .. ..$ chromosome: int(0) 740s .. ..$ start : num(0) 740s .. ..$ end : num(0) 740s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.011 0 0.011 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s DH segmentation (locally-indexed) rows: 740s [1] startRow endRow 740s <0 rows> (or 0-length row.names) 740s int(0) 740s DH segmentation rows: 740s [1] startRow endRow 740s <0 rows> (or 0-length row.names) 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s NA NA NA NA NA 740s startRow endRow 740s NA NA NA 740s Rows: 740s [1] 2 740s TCN segmentation rows: 740s startRow endRow 740s 2 NA NA 740s TCN and DH segmentation rows: 740s startRow endRow 740s 2 NA NA 740s startRow endRow 740s NA NA NA 740s startRow endRow 740s 1 1 7586 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s 4 10268 14658 740s startRow endRow 740s 1 10 7574 740s 2 NA NA 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 2 1 120908859 142693887 0 NA 0 0 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 2 2 1 1 120908859 142693887 0 NA 0 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 2 0 NA NA NA NA 740s Total CN segment #2 ([1.20909e+08,1.42694e+08]) of 4...done 740s Total CN segment #3 ([1.42694e+08,1.8545e+08]) of 4... 740s Number of TCN loci in segment: 2681 740s Locus data for TCN segment: 740s 'data.frame': 2681 obs. of 9 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 740s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 740s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 740s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 740s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 740s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 740s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 740s $ rho : num 0.117 0.258 NA NA NA ... 740s Number of loci: 2681 740s Number of SNPs: 777 (28.98%) 740s Number of heterozygous SNPs: 777 (100.00%) 740s Chromosome: 1 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 1 740s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 2681 obs. of 4 variables: 740s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 740s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 740s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 1 740s ..$ start : num 1.43e+08 740s ..$ end : num 1.85e+08 740s ..$ nbrOfLoci : int 777 740s ..$ mean : num 0.0973 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 1 740s ..$ endRow : int 2677 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 1 740s .. ..$ start : num 1.43e+08 740s .. ..$ end : num 1.85e+08 740s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.067 0.001 0.068 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 1 2677 740s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 7587 10263 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 142693888 185449813 777 0.0973 740s startRow endRow 740s 1 7587 10263 740s Rows: 740s [1] 3 740s TCN segmentation rows: 740s startRow endRow 740s 3 7587 10267 740s TCN and DH segmentation rows: 740s startRow endRow 740s 3 7587 10267 740s startRow endRow 740s 1 7587 10263 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s 4 10268 14658 740s startRow endRow 740s 1 10 7574 740s 2 NA NA 740s 3 7587 10263 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 3 1 142693888 185449813 2681 2.0689 777 777 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 3 3 1 1 142693888 185449813 2681 2.0689 777 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 3 777 142693888 185449813 777 0.0973 740s Total CN segment #3 ([1.42694e+08,1.8545e+08]) of 4...done 740s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4... 740s Number of TCN loci in segment: 4391 740s Locus data for TCN segment: 740s 'data.frame': 4391 obs. of 9 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 740s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 740s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 740s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 740s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 740s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 740s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 740s $ rho : num NA 0.2186 NA 0.0503 NA ... 740s Number of loci: 4391 740s Number of SNPs: 1311 (29.86%) 740s Number of heterozygous SNPs: 1311 (100.00%) 740s Chromosome: 1 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 1 740s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 4391 obs. of 4 variables: 740s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 740s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 740s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 1 740s ..$ start : num 1.85e+08 740s ..$ end : num 2.47e+08 740s ..$ nbrOfLoci : int 1311 740s ..$ mean : num 0.23 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 2 740s ..$ endRow : int 4388 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 1 740s .. ..$ start : num 1.85e+08 740s .. ..$ end : num 2.47e+08 740s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.05 0 0.05 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 2 4388 740s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 10269 14655 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 185449813 247137334 1311 0.2295 740s startRow endRow 740s 1 10269 14655 740s Rows: 740s [1] 4 740s TCN segmentation rows: 740s startRow endRow 740s 4 10268 14658 740s TCN and DH segmentation rows: 740s startRow endRow 740s 4 10268 14658 740s startRow endRow 740s 1 10269 14655 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s 4 10268 14658 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s 4 10268 14658 740s startRow endRow 740s 1 10 7574 740s 2 NA NA 740s 3 7587 10263 740s 4 10269 14655 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s 4 10268 14658 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 4 1 185449813 247137334 4391 2.6341 1311 1311 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 4 4 1 1 185449813 247137334 4391 2.6341 1311 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 4 1311 185449813 247137334 1311 0.2295 740s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 120908858 7586 1.3853 2108 740s 2 1 2 1 120908859 142693887 0 NA 0 740s 3 1 3 1 142693888 185449813 2681 2.0689 777 740s 4 1 4 1 185449813 247137334 4391 2.6341 1311 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 1 2108 554484 120908858 2108 0.5116 740s 2 0 NA NA NA NA 740s 3 777 142693888 185449813 777 0.0973 740s 4 1311 185449813 247137334 1311 0.2295 740s Calculating (C1,C2) per segment... 740s Calculating (C1,C2) per segment...done 740s Number of segments: 4 740s Segmenting paired tumor-normal signals using Paired PSCBS...done 740s Post-segmenting TCNs... 740s Number of segments: 4 740s Number of chromosomes: 1 740s [1] 1 740s Chromosome 1 ('chr01') of 1... 740s Rows: 740s [1] 1 2 3 4 740s Number of segments: 4 740s TCN segment #1 ('1') of 4... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #1 ('1') of 4...done 740s TCN segment #2 ('2') of 4... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #2 ('2') of 4...done 740s TCN segment #3 ('3') of 4... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #3 ('3') of 4...done 740s TCN segment #4 ('4') of 4... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #4 ('4') of 4...done 740s Chromosome 1 ('chr01') of 1...done 740s Update (C1,C2) per segment... 740s Update (C1,C2) per segment...done 740s Post-segmenting TCNs...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 120908858 7586 1.3853 2108 740s 2 1 2 1 120908859 142693887 0 NA 0 740s 3 1 3 1 142693888 185449813 2681 2.0689 777 740s 4 1 4 1 185449813 247137334 4391 2.6341 1311 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 740s 2 0 NA NA NA NA NA NA 740s 3 777 142693888 185449813 777 0.0973 0.9337980 1.135102 740s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 120908858 7586 1.3853 2108 740s 2 1 2 1 120908859 142693887 0 NA 0 740s 3 1 3 1 142693888 185449813 2681 2.0689 777 740s 4 1 4 1 185449813 247137334 4391 2.6341 1311 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 740s 2 0 NA NA NA NA NA NA 740s 3 777 142693888 185449813 777 0.0973 0.9337980 1.135102 740s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 740s - segmentByPairedPSCBS() w/ known segments using 'multisession' futures ... 740s Segmenting paired tumor-normal signals using Paired PSCBS... 740s Calling genotypes from normal allele B fractions... 740s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 740s Called genotypes: 740s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 740s - attr(*, "modelFit")=List of 1 740s ..$ :List of 7 740s .. ..$ flavor : chr "density" 740s .. ..$ cn : int 2 740s .. ..$ nbrOfGenotypeGroups: int 3 740s .. ..$ tau : num [1:2] 0.315 0.677 740s .. ..$ n : int 14640 740s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 740s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 740s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 740s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 740s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 740s .. .. ..$ type : chr [1:2] "valley" "valley" 740s .. .. ..$ x : num [1:2] 0.315 0.677 740s .. .. ..$ density: num [1:2] 0.522 0.552 740s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 740s muN 740s 0 0.5 1 740s 5221 4198 5251 740s Calling genotypes from normal allele B fractions...done 740s Normalizing betaT using betaN (TumorBoost)... 740s Normalized BAFs: 740s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 740s - attr(*, "modelFit")=List of 5 740s ..$ method : chr "normalizeTumorBoost" 740s ..$ flavor : chr "v4" 740s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 740s .. ..- attr(*, "modelFit")=List of 1 740s .. .. ..$ :List of 7 740s .. .. .. ..$ flavor : chr "density" 740s .. .. .. ..$ cn : int 2 740s .. .. .. ..$ nbrOfGenotypeGroups: int 3 740s .. .. .. ..$ tau : num [1:2] 0.315 0.677 740s .. .. .. ..$ n : int 14640 740s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 740s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 740s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 740s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 740s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 740s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 740s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 740s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 740s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 740s ..$ preserveScale: logi FALSE 740s ..$ scaleFactor : num NA 740s Normalizing betaT using betaN (TumorBoost)...done 740s Setup up data... 740s 'data.frame': 14670 obs. of 7 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 740s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 740s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 740s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 740s ..- attr(*, "modelFit")=List of 5 740s .. ..$ method : chr "normalizeTumorBoost" 740s .. ..$ flavor : chr "v4" 740s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 740s .. .. ..- attr(*, "modelFit")=List of 1 740s .. .. .. ..$ :List of 7 740s .. .. .. .. ..$ flavor : chr "density" 740s .. .. .. .. ..$ cn : int 2 740s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 740s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 740s .. .. .. .. ..$ n : int 14640 740s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 740s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 740s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 740s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 740s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 740s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 740s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 740s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 740s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 740s .. ..$ preserveScale: logi FALSE 740s .. ..$ scaleFactor : num NA 740s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 740s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 740s ..- attr(*, "modelFit")=List of 1 740s .. ..$ :List of 7 740s .. .. ..$ flavor : chr "density" 740s .. .. ..$ cn : int 2 740s .. .. ..$ nbrOfGenotypeGroups: int 3 740s .. .. ..$ tau : num [1:2] 0.315 0.677 740s .. .. ..$ n : int 14640 740s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 740s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 740s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 740s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 740s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 740s .. .. .. ..$ type : chr [1:2] "valley" "valley" 740s .. .. .. ..$ x : num [1:2] 0.315 0.677 740s .. .. .. ..$ density: num [1:2] 0.522 0.552 740s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 740s Setup up data...done 740s Dropping loci for which TCNs are missing... 740s Number of loci dropped: 12 740s Dropping loci for which TCNs are missing...done 740s Ordering data along genome... 740s 'data.frame': 14658 obs. of 7 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s Ordering data along genome...done 740s Keeping only current chromosome for 'knownSegments'... 740s Chromosome: 1 740s Known segments for this chromosome: 740s chromosome start end length 740s 1 1 -Inf 120908858 Inf 740s 2 1 120908859 142693887 21785028 740s 3 1 142693888 Inf Inf 740s Keeping only current chromosome for 'knownSegments'...done 740s alphaTCN: 0.009 740s alphaDH: 0.001 740s Number of loci: 14658 740s Calculating DHs... 740s Number of SNPs: 14658 740s Number of heterozygous SNPs: 4196 (28.63%) 740s Normalized DHs: 740s num [1:14658] NA NA NA NA NA ... 740s Calculating DHs...done 740s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 740s Produced 2 seeds from this stream for future usage 740s Identification of change points by total copy numbers... 740s Segmenting by CBS... 740s Chromosome: 1 740s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 740s Produced 3 seeds from this stream for future usage 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 14658 obs. of 4 variables: 740s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 740s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 740s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 4 obs. of 6 variables: 740s ..$ sampleName: chr [1:4] NA NA NA NA 740s ..$ chromosome: int [1:4] 1 1 1 1 740s ..$ start : num [1:4] 5.54e+05 1.21e+08 1.43e+08 1.85e+08 740s ..$ end : num [1:4] 1.21e+08 1.43e+08 1.85e+08 2.47e+08 740s ..$ nbrOfLoci : int [1:4] 7586 0 2681 4391 740s ..$ mean : num [1:4] 1.39 NA 2.07 2.63 740s $ segRows:'data.frame': 4 obs. of 2 variables: 740s ..$ startRow: int [1:4] 1 NA 7587 10268 740s ..$ endRow : int [1:4] 7586 NA 10267 14658 740s $ params :List of 5 740s ..$ alpha : num 0.009 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 4 obs. of 3 variables: 740s .. ..$ chromosome: int [1:4] 1 1 2 1 740s .. ..$ start : num [1:4] -Inf -Inf -Inf 1.43e+08 740s .. ..$ end : num [1:4] 1.21e+08 Inf Inf Inf 740s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.714 0.001 0.717 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s Identification of change points by total copy numbers...done 740s Restructure TCN segmentation results... 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 740s 1 1 554484 120908858 7586 1.3853 740s 2 1 120908859 142693887 0 NA 740s 3 1 142693888 185449813 2681 2.0689 740s 4 1 185449813 247137334 4391 2.6341 740s Number of TCN segments: 4 740s Restructure TCN segmentation results...done 740s Total CN segment #1 ([ 554484,1.20909e+08]) of 4... 740s Number of TCN loci in segment: 7586 740s Locus data for TCN segment: 740s 'data.frame': 7586 obs. of 9 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 554484 730720 782343 878522 916294 ... 740s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 740s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 740s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 740s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 740s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 740s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 740s $ rho : num NA NA NA NA NA ... 740s Number of loci: 7586 740s Number of SNPs: 2108 (27.79%) 740s Number of heterozygous SNPs: 2108 (100.00%) 740s Chromosome: 1 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 1 740s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 7586 obs. of 4 variables: 740s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 740s ..$ y : num [1:7586] NA NA NA NA NA ... 740s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 1 740s ..$ start : num 554484 740s ..$ end : num 1.21e+08 740s ..$ nbrOfLoci : int 2108 740s ..$ mean : num 0.512 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 10 740s ..$ endRow : int 7574 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 1 740s .. ..$ start : num 554484 740s .. ..$ end : num 1.21e+08 740s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.205 0.004 0.365 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 10 7574 740s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 10 7574 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 554484 120908858 2108 0.5116 740s startRow endRow 740s 1 10 7574 740s Rows: 740s [1] 1 740s TCN segmentation rows: 740s startRow endRow 740s 1 1 7586 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7586 740s startRow endRow 740s 1 10 7574 740s NULL 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7586 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s 4 10268 14658 740s startRow endRow 740s 1 10 7574 740s startRow endRow 740s 1 1 7586 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 1 1 554484 120908858 7586 1.3853 2108 2108 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 120908858 7586 1.3853 2108 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 1 2108 554484 120908858 2108 0.5116 740s Total CN segment #1 ([ 554484,1.20909e+08]) of 4...done 740s Total CN segment #2 ([1.20909e+08,1.42694e+08]) of 4... 740s Number of TCN loci in segment: 0 740s Locus data for TCN segment: 740s 'data.frame': 0 obs. of 9 variables: 740s $ chromosome: int 740s $ x : num 740s $ CT : num 740s $ betaT : num 740s $ betaTN : num 740s $ betaN : num 740s $ muN : num 740s $ index : int 740s $ rho : num 740s Number of loci: 0 740s Number of SNPs: 0 (NaN%) 740s Number of heterozygous SNPs: 0 (NaN%) 740s Chromosome: 1 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: NA 740s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 0 obs. of 4 variables: 740s ..$ chromosome: int(0) 740s ..$ x : num(0) 740s ..$ y : num(0) 740s ..$ index : int(0) 740s $ output :'data.frame': 0 obs. of 6 variables: 740s ..$ sampleName: chr(0) 740s ..$ chromosome: num(0) 740s ..$ start : num(0) 740s ..$ end : num(0) 740s ..$ nbrOfLoci : int(0) 740s ..$ mean : num(0) 740s $ segRows:'data.frame': 0 obs. of 2 variables: 740s ..$ startRow: int(0) 740s ..$ endRow : int(0) 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 0 obs. of 3 variables: 740s .. ..$ chromosome: int(0) 740s .. ..$ start : num(0) 740s .. ..$ end : num(0) 740s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.009 0 0.009 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s DH segmentation (locally-indexed) rows: 740s [1] startRow endRow 740s <0 rows> (or 0-length row.names) 740s int(0) 740s DH segmentation rows: 740s [1] startRow endRow 740s <0 rows> (or 0-length row.names) 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s NA NA NA NA NA 740s startRow endRow 740s NA NA NA 740s Rows: 740s [1] 2 740s TCN segmentation rows: 740s startRow endRow 740s 2 NA NA 740s TCN and DH segmentation rows: 740s startRow endRow 740s 2 NA NA 740s startRow endRow 740s NA NA NA 740s startRow endRow 740s 1 1 7586 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s 4 10268 14658 740s startRow endRow 740s 1 10 7574 740s 2 NA NA 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 2 1 120908859 142693887 0 NA 0 0 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 2 2 1 1 120908859 142693887 0 NA 0 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 2 0 NA NA NA NA 740s Total CN segment #2 ([1.20909e+08,1.42694e+08]) of 4...done 740s Total CN segment #3 ([1.42694e+08,1.8545e+08]) of 4... 740s Number of TCN loci in segment: 2681 740s Locus data for TCN segment: 740s 'data.frame': 2681 obs. of 9 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 740s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 740s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 740s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 740s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 740s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 740s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 740s $ rho : num 0.117 0.258 NA NA NA ... 740s Number of loci: 2681 740s Number of SNPs: 777 (28.98%) 740s Number of heterozygous SNPs: 777 (100.00%) 740s Chromosome: 1 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 1 740s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 2681 obs. of 4 variables: 740s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 740s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 740s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 1 740s ..$ start : num 1.43e+08 740s ..$ end : num 1.85e+08 740s ..$ nbrOfLoci : int 777 740s ..$ mean : num 0.0973 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 1 740s ..$ endRow : int 2677 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 1 740s .. ..$ start : num 1.43e+08 740s .. ..$ end : num 1.85e+08 740s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.066 0.001 0.066 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 1 2677 740s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 7587 10263 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 142693888 185449813 777 0.0973 740s startRow endRow 740s 1 7587 10263 740s Rows: 740s [1] 3 740s TCN segmentation rows: 740s startRow endRow 740s 3 7587 10267 740s TCN and DH segmentation rows: 740s startRow endRow 740s 3 7587 10267 740s startRow endRow 740s 1 7587 10263 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s 4 10268 14658 740s startRow endRow 740s 1 10 7574 740s 2 NA NA 740s 3 7587 10263 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 3 1 142693888 185449813 2681 2.0689 777 777 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 3 3 1 1 142693888 185449813 2681 2.0689 777 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 3 777 142693888 185449813 777 0.0973 740s Total CN segment #3 ([1.42694e+08,1.8545e+08]) of 4...done 740s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4... 740s Number of TCN loci in segment: 4391 740s Locus data for TCN segment: 740s 'data.frame': 4391 obs. of 9 variables: 740s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 740s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 740s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 740s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 740s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 740s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 740s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 740s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 740s $ rho : num NA 0.2186 NA 0.0503 NA ... 740s Number of loci: 4391 740s Number of SNPs: 1311 (29.86%) 740s Number of heterozygous SNPs: 1311 (100.00%) 740s Chromosome: 1 740s Segmenting DH signals... 740s Segmenting by CBS... 740s Chromosome: 1 740s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 740s Segmenting by CBS...done 740s List of 4 740s $ data :'data.frame': 4391 obs. of 4 variables: 740s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 740s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 740s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 740s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 740s $ output :'data.frame': 1 obs. of 6 variables: 740s ..$ sampleName: chr NA 740s ..$ chromosome: int 1 740s ..$ start : num 1.85e+08 740s ..$ end : num 2.47e+08 740s ..$ nbrOfLoci : int 1311 740s ..$ mean : num 0.23 740s $ segRows:'data.frame': 1 obs. of 2 variables: 740s ..$ startRow: int 2 740s ..$ endRow : int 4388 740s $ params :List of 5 740s ..$ alpha : num 0.001 740s ..$ undo : num 0 740s ..$ joinSegments : logi TRUE 740s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 740s .. ..$ chromosome: int 1 740s .. ..$ start : num 1.85e+08 740s .. ..$ end : num 2.47e+08 740s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 740s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.05 0 0.05 0 0 740s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 740s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 740s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 740s DH segmentation (locally-indexed) rows: 740s startRow endRow 740s 1 2 4388 740s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 740s DH segmentation rows: 740s startRow endRow 740s 1 10269 14655 740s Segmenting DH signals...done 740s DH segmentation table: 740s dhStart dhEnd dhNbrOfLoci dhMean 740s 1 185449813 247137334 1311 0.2295 740s startRow endRow 740s 1 10269 14655 740s Rows: 740s [1] 4 740s TCN segmentation rows: 740s startRow endRow 740s 4 10268 14658 740s TCN and DH segmentation rows: 740s startRow endRow 740s 4 10268 14658 740s startRow endRow 740s 1 10269 14655 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s TCN segmentation (expanded) rows: 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s 4 10268 14658 740s TCN and DH segmentation rows: 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s 4 10268 14658 740s startRow endRow 740s 1 10 7574 740s 2 NA NA 740s 3 7587 10263 740s 4 10269 14655 740s startRow endRow 740s 1 1 7586 740s 2 NA NA 740s 3 7587 10267 740s 4 10268 14658 740s Total CN segmentation table (expanded): 740s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 740s 4 1 185449813 247137334 4391 2.6341 1311 1311 740s (TCN,DH) segmentation for one total CN segment: 740s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 4 4 1 1 185449813 247137334 4391 2.6341 1311 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 4 1311 185449813 247137334 1311 0.2295 740s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 120908858 7586 1.3853 2108 740s 2 1 2 1 120908859 142693887 0 NA 0 740s 3 1 3 1 142693888 185449813 2681 2.0689 777 740s 4 1 4 1 185449813 247137334 4391 2.6341 1311 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 740s 1 2108 554484 120908858 2108 0.5116 740s 2 0 NA NA NA NA 740s 3 777 142693888 185449813 777 0.0973 740s 4 1311 185449813 247137334 1311 0.2295 740s Calculating (C1,C2) per segment... 740s Calculating (C1,C2) per segment...done 740s Number of segments: 4 740s Segmenting paired tumor-normal signals using Paired PSCBS...done 740s Post-segmenting TCNs... 740s Number of segments: 4 740s Number of chromosomes: 1 740s [1] 1 740s Chromosome 1 ('chr01') of 1... 740s Rows: 740s [1] 1 2 3 4 740s Number of segments: 4 740s TCN segment #1 ('1') of 4... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #1 ('1') of 4...done 740s TCN segment #2 ('2') of 4... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #2 ('2') of 4...done 740s TCN segment #3 ('3') of 4... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #3 ('3') of 4...done 740s TCN segment #4 ('4') of 4... 740s Nothing todo. Only one DH segmentation. Skipping. 740s TCN segment #4 ('4') of 4...done 740s Chromosome 1 ('chr01') of 1...done 740s Update (C1,C2) per segment... 740s Update (C1,C2) per segment...done 740s Post-segmenting TCNs...done 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 120908858 7586 1.3853 2108 740s 2 1 2 1 120908859 142693887 0 NA 0 740s 3 1 3 1 142693888 185449813 2681 2.0689 777 740s 4 1 4 1 185449813 247137334 4391 2.6341 1311 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 740s 2 0 NA NA NA NA NA NA 740s 3 777 142693888 185449813 777 0.0973 0.9337980 1.135102 740s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 740s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 740s 1 1 1 1 554484 120908858 7586 1.3853 2108 740s 2 1 2 1 120908859 142693887 0 NA 0 740s 3 1 3 1 142693888 185449813 2681 2.0689 777 740s 4 1 4 1 185449813 247137334 4391 2.6341 1311 740s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 740s 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 740s 2 0 NA NA NA NA NA NA 740s 3 777 142693888 185449813 777 0.0973 0.9337980 1.135102 740s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 740s > 740s > message("*** segmentByPairedPSCBS() via futures ... DONE") 740s *** segmentByPairedPSCBS() via futures ... DONE 740s > 740s > 740s > ## Cleanup 740s > plan(oplan) 740s > rm(list=c("fits", "data", "fit")) 740s > 740s > proc.time() 740s user system elapsed 740s 46.565 1.312 48.590 740s Test segmentByPairedPSCBS,futures passed 740s 0 740s Begin test segmentByPairedPSCBS,noNormalBAFs 740s + [ 0 != 0 ] 740s + echo Test segmentByPairedPSCBS,futures passed 740s + echo 0 740s + echo Begin test segmentByPairedPSCBS,noNormalBAFs 740s + exitcode=0 740s + R CMD BATCH segmentByPairedPSCBS,noNormalBAFs.R 759s + cat segmentByPairedPSCBS,noNormalBAFs.Rout 759s 759s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 759s Copyright (C) 2024 The R Foundation for Statistical Computing 759s Platform: aarch64-unknown-linux-gnu (64-bit) 759s 759s R is free software and comes with ABSOLUTELY NO WARRANTY. 759s You are welcome to redistribute it under certain conditions. 759s Type 'license()' or 'licence()' for distribution details. 759s 759s R is a collaborative project with many contributors. 759s Type 'contributors()' for more information and 759s 'citation()' on how to cite R or R packages in publications. 759s 759s Type 'demo()' for some demos, 'help()' for on-line help, or 759s 'help.start()' for an HTML browser interface to help. 759s Type 'q()' to quit R. 759s 759s [Previously saved workspace restored] 759s 759s > library("PSCBS") 759s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 759s 759s Attaching package: 'PSCBS' 759s 759s The following objects are masked from 'package:base': 759s 759s append, load 759s 759s > 759s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 759s > # Load SNP microarray data 759s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 759s > data <- PSCBS::exampleData("paired.chr01") 759s > str(data) 759s 'data.frame': 73346 obs. of 6 variables: 759s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 759s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 759s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 759s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 759s $ CN : num 2.36 2.13 2.59 1.93 1.71 ... 759s $ betaN : num 0.827 0.875 0.887 0.884 0.103 ... 759s > 759s > # Drop single-locus outliers 759s > dataS <- dropSegmentationOutliers(data) 759s > 759s > # Run light-weight tests by default 759s > if (Sys.getenv("_R_CHECK_FULL_") == "") { 759s + # Use only every 5th data point 759s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 759s + # Number of segments (for assertion) 759s + nSegs <- 3L 759s + # Number of bootstrap samples (see below) 759s + B <- 100L 759s + } else { 759s + # Full tests 759s + nSegs <- 8L 759s + B <- 1000L 759s + } 759s > 759s > str(dataS) 759s 'data.frame': 14670 obs. of 6 variables: 759s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 759s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 759s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 759s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 759s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 759s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 759s > 759s > R.oo::attachLocally(dataS) 759s > 759s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 759s > # Simulate that genotypes are known by other means 759s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 759s > library("aroma.light") 759s aroma.light v3.32.0 (2023-10-24) successfully loaded. See ?aroma.light for help. 759s > muN <- aroma.light::callNaiveGenotypes(betaN, censorAt=c(0,1)) 759s > 759s > 759s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 759s > # Paired PSCBS segmentation 759s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 759s > fit <- segmentByPairedPSCBS(CT, betaT=betaT, muN=muN, tbn=FALSE, 759s + chromosome=chromosome, x=x, 759s + seed=0xBEEF, verbose=-10) 759s Segmenting paired tumor-normal signals using Paired PSCBS... 759s Setup up data... 759s 'data.frame': 14670 obs. of 6 variables: 759s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 759s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 759s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 759s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 759s $ betaTN : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 759s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 759s ..- attr(*, "modelFit")=List of 1 759s .. ..$ :List of 7 759s .. .. ..$ flavor : chr "density" 759s .. .. ..$ cn : int 2 759s .. .. ..$ nbrOfGenotypeGroups: int 3 759s .. .. ..$ tau : num [1:2] 0.315 0.677 759s .. .. ..$ n : int 14640 759s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 759s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 759s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 759s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 759s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 759s .. .. .. ..$ type : chr [1:2] "valley" "valley" 759s .. .. .. ..$ x : num [1:2] 0.315 0.677 759s .. .. .. ..$ density: num [1:2] 0.522 0.552 759s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 759s Setup up data...done 759s Dropping loci for which TCNs are missing... 759s Number of loci dropped: 12 759s Dropping loci for which TCNs are missing...done 759s Ordering data along genome... 759s 'data.frame': 14658 obs. of 6 variables: 759s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 759s $ x : num 554484 730720 782343 878522 916294 ... 759s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 759s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 759s $ betaTN : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 759s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 759s Ordering data along genome...done 759s Keeping only current chromosome for 'knownSegments'... 759s Chromosome: 1 759s Known segments for this chromosome: 759s [1] chromosome start end 759s <0 rows> (or 0-length row.names) 759s Keeping only current chromosome for 'knownSegments'...done 759s alphaTCN: 0.009 759s alphaDH: 0.001 759s Number of loci: 14658 759s Calculating DHs... 759s Number of SNPs: 14658 759s Number of heterozygous SNPs: 4196 (28.63%) 759s Normalized DHs: 759s num [1:14658] NA NA NA NA NA ... 759s Calculating DHs...done 759s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 759s Produced 2 seeds from this stream for future usage 759s Identification of change points by total copy numbers... 759s Segmenting by CBS... 759s Chromosome: 1 759s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 759s Segmenting by CBS...done 759s List of 4 759s $ data :'data.frame': 14658 obs. of 4 variables: 759s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 759s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 759s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 759s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 759s $ output :'data.frame': 3 obs. of 6 variables: 759s ..$ sampleName: chr [1:3] NA NA NA 759s ..$ chromosome: int [1:3] 1 1 1 759s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 759s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 759s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 759s ..$ mean : num [1:3] 1.39 2.07 2.63 759s $ segRows:'data.frame': 3 obs. of 2 variables: 759s ..$ startRow: int [1:3] 1 7600 10268 759s ..$ endRow : int [1:3] 7599 10267 14658 759s $ params :List of 5 759s ..$ alpha : num 0.009 759s ..$ undo : num 0 759s ..$ joinSegments : logi TRUE 759s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 759s .. ..$ chromosome: int 1 759s .. ..$ start : num -Inf 759s .. ..$ end : num Inf 759s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 759s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 759s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 1.83 0 1.83 0 0 759s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 759s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 759s - attr(*, "randomSeed")= int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 759s Identification of change points by total copy numbers...done 759s Restructure TCN segmentation results... 759s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 759s 1 1 554484 143926517 7599 1.3859 759s 2 1 143926517 185449813 2668 2.0704 759s 3 1 185449813 247137334 4391 2.6341 759s Number of TCN segments: 3 759s Restructure TCN segmentation results...done 759s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 759s Number of TCN loci in segment: 7599 759s Locus data for TCN segment: 759s 'data.frame': 7599 obs. of 8 variables: 759s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 759s $ x : num 554484 730720 782343 878522 916294 ... 759s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 759s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 759s $ betaTN : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 759s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 759s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 759s $ rho : num NA NA NA NA NA ... 759s Number of loci: 7599 759s Number of SNPs: 2111 (27.78%) 759s Number of heterozygous SNPs: 2111 (100.00%) 759s Chromosome: 1 759s Segmenting DH signals... 759s Segmenting by CBS... 759s Chromosome: 1 759s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 759s Segmenting by CBS...done 759s List of 4 759s $ data :'data.frame': 7599 obs. of 4 variables: 759s ..$ chromosome: int [1:7599] 1 1 1 1 1 1 1 1 1 1 ... 759s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 759s ..$ y : num [1:7599] NA NA NA NA NA ... 759s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 759s $ output :'data.frame': 1 obs. of 6 variables: 759s ..$ sampleName: chr NA 759s ..$ chromosome: int 1 759s ..$ start : num 554484 759s ..$ end : num 1.44e+08 759s ..$ nbrOfLoci : int 2111 759s ..$ mean : num 0.524 759s $ segRows:'data.frame': 1 obs. of 2 variables: 759s ..$ startRow: int 10 759s ..$ endRow : int 7594 759s $ params :List of 5 759s ..$ alpha : num 0.001 759s ..$ undo : num 0 759s ..$ joinSegments : logi TRUE 759s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 759s .. ..$ chromosome: int 1 759s .. ..$ start : num 554484 759s .. ..$ end : num 1.44e+08 759s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 759s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 759s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.299 0.009 0.31 0 0 759s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 759s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 759s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 759s DH segmentation (locally-indexed) rows: 759s startRow endRow 759s 1 10 7594 759s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 759s DH segmentation rows: 759s startRow endRow 759s 1 10 7594 759s Segmenting DH signals...done 759s DH segmentation table: 759s dhStart dhEnd dhNbrOfLoci dhMean 759s 1 554484 143926517 2111 0.5237 759s startRow endRow 759s 1 10 7594 759s Rows: 759s [1] 1 759s TCN segmentation rows: 759s startRow endRow 759s 1 1 7599 759s TCN and DH segmentation rows: 759s startRow endRow 759s 1 1 7599 759s startRow endRow 759s 1 10 7594 759s NULL 759s TCN segmentation (expanded) rows: 759s startRow endRow 759s 1 1 7599 759s TCN and DH segmentation rows: 759s startRow endRow 759s 1 1 7599 759s 2 7600 10267 759s 3 10268 14658 759s startRow endRow 759s 1 10 7594 759s startRow endRow 759s 1 1 7599 759s Total CN segmentation table (expanded): 759s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 759s 1 1 554484 143926517 7599 1.3859 2111 2111 759s (TCN,DH) segmentation for one total CN segment: 759s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 759s 1 1 1 1 554484 143926517 7599 1.3859 2111 759s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 759s 1 2111 554484 143926517 2111 0.5237 759s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 759s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 759s Number of TCN loci in segment: 2668 759s Locus data for TCN segment: 759s 'data.frame': 2668 obs. of 8 variables: 759s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 759s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 759s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 759s $ betaT : num 0.1899 0.909 0.9166 0.1668 0.0308 ... 759s $ betaTN : num 0.1899 0.909 0.9166 0.1668 0.0308 ... 759s $ muN : num 0 1 1 0 0 1 0 0 0 0 ... 759s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 759s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 759s Number of loci: 2668 759s Number of SNPs: 774 (29.01%) 759s Number of heterozygous SNPs: 774 (100.00%) 759s Chromosome: 1 759s Segmenting DH signals... 759s Segmenting by CBS... 759s Chromosome: 1 759s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 759s Segmenting by CBS...done 759s List of 4 759s $ data :'data.frame': 2668 obs. of 4 variables: 759s ..$ chromosome: int [1:2668] 1 1 1 1 1 1 1 1 1 1 ... 759s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 759s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 759s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 759s $ output :'data.frame': 1 obs. of 6 variables: 759s ..$ sampleName: chr NA 759s ..$ chromosome: int 1 759s ..$ start : num 1.44e+08 759s ..$ end : num 1.85e+08 759s ..$ nbrOfLoci : int 774 759s ..$ mean : num 0.154 759s $ segRows:'data.frame': 1 obs. of 2 variables: 759s ..$ startRow: int 15 759s ..$ endRow : int 2664 759s $ params :List of 5 759s ..$ alpha : num 0.001 759s ..$ undo : num 0 759s ..$ joinSegments : logi TRUE 759s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 759s .. ..$ chromosome: int 1 759s .. ..$ start : num 1.44e+08 759s .. ..$ end : num 1.85e+08 759s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 759s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 759s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.116 0.003 0.12 0 0 759s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 759s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 759s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 759s DH segmentation (locally-indexed) rows: 759s startRow endRow 759s 1 15 2664 759s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 759s DH segmentation rows: 759s startRow endRow 759s 1 7614 10263 759s Segmenting DH signals...done 759s DH segmentation table: 759s dhStart dhEnd dhNbrOfLoci dhMean 759s 1 143926517 185449813 774 0.1542 759s startRow endRow 759s 1 7614 10263 759s Rows: 759s [1] 2 759s TCN segmentation rows: 759s startRow endRow 759s 2 7600 10267 759s TCN and DH segmentation rows: 759s startRow endRow 759s 2 7600 10267 759s startRow endRow 759s 1 7614 10263 759s startRow endRow 759s 1 1 7599 759s TCN segmentation (expanded) rows: 759s startRow endRow 759s 1 1 7599 759s 2 7600 10267 759s TCN and DH segmentation rows: 759s startRow endRow 759s 1 1 7599 759s 2 7600 10267 759s 3 10268 14658 759s startRow endRow 759s 1 10 7594 759s 2 7614 10263 759s startRow endRow 759s 1 1 7599 759s 2 7600 10267 759s Total CN segmentation table (expanded): 759s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 759s 2 1 143926517 185449813 2668 2.0704 774 774 759s (TCN,DH) segmentation for one total CN segment: 759s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 759s 2 2 1 1 143926517 185449813 2668 2.0704 774 759s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 759s 2 774 143926517 185449813 774 0.1542 759s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 759s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 759s Number of TCN loci in segment: 4391 759s Locus data for TCN segment: 759s 'data.frame': 4391 obs. of 8 variables: 759s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 759s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 759s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 759s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 759s $ betaTN : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 759s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 759s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 759s $ rho : num NA 0.0308 NA 0.2533 NA ... 759s Number of loci: 4391 759s Number of SNPs: 1311 (29.86%) 759s Number of heterozygous SNPs: 1311 (100.00%) 759s Chromosome: 1 759s Segmenting DH signals... 759s Segmenting by CBS... 759s Chromosome: 1 759s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 759s Segmenting by CBS...done 759s List of 4 759s $ data :'data.frame': 4391 obs. of 4 variables: 759s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 759s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 759s ..$ y : num [1:4391] NA 0.0308 NA 0.2533 NA ... 759s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 759s $ output :'data.frame': 1 obs. of 6 variables: 759s ..$ sampleName: chr NA 759s ..$ chromosome: int 1 759s ..$ start : num 1.85e+08 759s ..$ end : num 2.47e+08 759s ..$ nbrOfLoci : int 1311 759s ..$ mean : num 0.251 759s $ segRows:'data.frame': 1 obs. of 2 variables: 759s ..$ startRow: int 2 759s ..$ endRow : int 4388 759s $ params :List of 5 759s ..$ alpha : num 0.001 759s ..$ undo : num 0 759s ..$ joinSegments : logi TRUE 759s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 759s .. ..$ chromosome: int 1 759s .. ..$ start : num 1.85e+08 759s .. ..$ end : num 2.47e+08 759s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 759s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 759s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.132 0 0.132 0 0 759s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 759s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 759s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 759s DH segmentation (locally-indexed) rows: 759s startRow endRow 759s 1 2 4388 759s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 759s DH segmentation rows: 759s startRow endRow 759s 1 10269 14655 759s Segmenting DH signals...done 759s DH segmentation table: 759s dhStart dhEnd dhNbrOfLoci dhMean 759s 1 185449813 247137334 1311 0.2512 759s startRow endRow 759s 1 10269 14655 759s Rows: 759s [1] 3 759s TCN segmentation rows: 759s startRow endRow 759s 3 10268 14658 759s TCN and DH segmentation rows: 759s startRow endRow 759s 3 10268 14658 759s startRow endRow 759s 1 10269 14655 759s startRow endRow 759s 1 1 7599 759s 2 7600 10267 759s TCN segmentation (expanded) rows: 759s startRow endRow 759s 1 1 7599 759s 2 7600 10267 759s 3 10268 14658 759s TCN and DH segmentation rows: 759s startRow endRow 759s 1 1 7599 759s 2 7600 10267 759s 3 10268 14658 759s startRow endRow 759s 1 10 7594 759s 2 7614 10263 759s 3 10269 14655 759s startRow endRow 759s 1 1 7599 759s 2 7600 10267 759s 3 10268 14658 759s Total CN segmentation table (expanded): 759s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 759s 3 1 185449813 247137334 4391 2.6341 1311 1311 759s (TCN,DH) segmentation for one total CN segment: 759s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 759s 3 3 1 1 185449813 247137334 4391 2.6341 1311 759s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 759s 3 1311 185449813 247137334 1311 0.2512 759s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 759s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 759s 1 1 1 1 554484 143926517 7599 1.3859 2111 759s 2 1 2 1 143926517 185449813 2668 2.0704 774 759s 3 1 3 1 185449813 247137334 4391 2.6341 1311 759s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 759s 1 2111 554484 143926517 2111 0.5237 759s 2 774 143926517 185449813 774 0.1542 759s 3 1311 185449813 247137334 1311 0.2512 759s Calculating (C1,C2) per segment... 759s Calculating (C1,C2) per segment...done 759s Number of segments: 3 759s Segmenting paired tumor-normal signals using Paired PSCBS...done 759s Post-segmenting TCNs... 759s Number of segments: 3 759s Number of chromosomes: 1 759s [1] 1 759s Chromosome 1 ('chr01') of 1... 759s Rows: 759s [1] 1 2 3 759s Number of segments: 3 759s TCN segment #1 ('1') of 3... 759s Nothing todo. Only one DH segmentation. Skipping. 759s TCN segment #1 ('1') of 3...done 759s TCN segment #2 ('2') of 3... 759s Nothing todo. Only one DH segmentation. Skipping. 759s TCN segment #2 ('2') of 3...done 759s TCN segment #3 ('3') of 3... 759s Nothing todo. Only one DH segmentation. Skipping. 759s TCN segment #3 ('3') of 3...done 759s Chromosome 1 ('chr01') of 1...done 759s Update (C1,C2) per segment... 759s Update (C1,C2) per segment...done 759s Post-segmenting TCNs...done 759s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 759s 1 1 1 1 554484 143926517 7599 1.3859 2111 759s 2 1 2 1 143926517 185449813 2668 2.0704 774 759s 3 1 3 1 185449813 247137334 4391 2.6341 1311 759s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 759s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 759s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 759s 3 1311 185449813 247137334 1311 0.2512 0.9862070 1.647893 759s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 759s 1 1 1 1 554484 143926517 7599 1.3859 2111 759s 2 1 2 1 143926517 185449813 2668 2.0704 774 759s 3 1 3 1 185449813 247137334 4391 2.6341 1311 759s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 759s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 759s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 759s 3 1311 185449813 247137334 1311 0.2512 0.9862070 1.647893 759s > print(fit) 759s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 759s 1 1 1 1 554484 143926517 7599 1.3859 2111 759s 2 1 2 1 143926517 185449813 2668 2.0704 774 759s 3 1 3 1 185449813 247137334 4391 2.6341 1311 759s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 759s 1 2111 2111 0.5237 0.3300521 1.055848 759s 2 774 774 0.1542 0.8755722 1.194828 759s 3 1311 1311 0.2512 0.9862070 1.647893 759s > 759s > # Plot results 759s > plotTracks(fit) 759s > 759s > # Sanity check 759s > stopifnot(nbrOfSegments(fit) == nSegs) 759s > 759s > 759s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 759s > # Bootstrap segment level estimates 759s > # (used by the AB caller, which, if skipped here, 759s > # will do it automatically) 759s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 759s > fit <- bootstrapTCNandDHByRegion(fit, B=B, verbose=-10) 759s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint... 759s Already done? 759s tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% dh_97.5% 759s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 759s c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% c2_97.5% 759s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 759s Bootstrapping (TCN,DH,C1,C2) segment mean levels... 759s Identifying heterozygous & homozygous SNPs and non-polymorphic loci... 759s Number of loci: 14658 759s Number of SNPs: 4196 759s Number of non-SNPs: 10462 759s Identifying heterozygous & homozygous SNPs and non-polymorphic loci...done 759s num [1:3, 1:100, 1:4] NA NA NA NA NA NA NA NA NA NA ... 759s - attr(*, "dimnames")=List of 3 759s ..$ : NULL 759s ..$ : NULL 759s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 759s Segment #1 (chr 1, tcnId=1, dhId=1) of 3... 759s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 759s 1 1 1 1 554484 143926517 7599 1.3859 2111 759s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 759s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 759s Number of TCNs: 7599 759s Number of DHs: 2111 759s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 759s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 759s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 759s Identify+ [ 0 != 0 ] 759s + echo Test segmentByPairedPSCBS,noNormalBAFs passed 759s + echo 0 759s + echo Begin test segmentByPairedPSCBS,report 759s + exitcode=0 759s + R CMD BATCH segmentByPairedPSCBS,report.R 759s loci used to bootstrap DH means... 759s Heterozygous SNPs to resample for DH: 759s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 759s Identify loci used to bootstrap DH means...done 759s Identify loci used to bootstrap TCN means... 759s SNPs: 759s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 759s Non-polymorphic loci: 759s int [1:5488] 1 2 3 4 5 6 7 8 9 11 ... 759s Heterozygous SNPs to resample for TCN: 759s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 759s Homozygous SNPs to resample for TCN: 759s int(0) 759s Non-polymorphic loci to resample for TCN: 759s int [1:5488] 1 2 3 4 5 6 7 8 9 11 ... 759s Heterozygous SNPs with non-DH to resample for TCN: 759s int(0) 759s Loci to resample for TCN: 759s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 759s Identify loci used to bootstrap TCN means...done 759s Number of (#hets, #homs, #nonSNPs): (2111,0,5488) 759s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 759s Number of bootstrap samples: 100 759s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 759s Segment #1 (chr 1, tcnId=1, dhId=1) of 3...done 759s Segment #2 (chr 1, tcnId=2, dhId=1) of 3... 759s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 759s 2 1 2 1 143926517 185449813 2668 2.0704 774 759s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 759s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 759s Number of TCNs: 2668 759s Number of DHs: 774 759s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 759s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 759s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 759s Identify loci used to bootstrap DH means... 759s Heterozygous SNPs to resample for DH: 759s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 759s Identify loci used to bootstrap DH means...done 759s Identify loci used to bootstrap TCN means... 759s SNPs: 759s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 759s Non-polymorphic loci: 759s int [1:1894] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 759s Heterozygous SNPs to resample for TCN: 759s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 759s Homozygous SNPs to resample for TCN: 759s int(0) 759s Non-polymorphic loci to resample for TCN: 759s int [1:1894] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 759s Heterozygous SNPs with non-DH to resample for TCN: 759s int(0) 759s Loci to resample for TCN: 759s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 759s Identify loci used to bootstrap TCN means...done 759s Number of (#hets, #homs, #nonSNPs): (774,0,1894) 759s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 759s Number of bootstrap samples: 100 759s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 759s Segment #2 (chr 1, tcnId=2, dhId=1) of 3...done 759s Segment #3 (chr 1, tcnId=3, dhId=1) of 3... 759s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 759s 3 1 3 1 185449813 247137334 4391 2.6341 1311 759s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 759s 3 1311 185449813 247137334 1311 0.2512 0.986207 1.647893 759s Number of TCNs: 4391 759s Number of DHs: 1311 759s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 759s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 759s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 759s Identify loci used to bootstrap DH means... 759s Heterozygous SNPs to resample for DH: 759s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 759s Identify loci used to bootstrap DH means...done 759s Identify loci used to bootstrap TCN means... 759s SNPs: 759s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 759s Non-polymorphic loci: 759s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 759s Heterozygous SNPs to resample for TCN: 759s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 759s Homozygous SNPs to resample for TCN: 759s int(0) 759s Non-polymorphic loci to resample for TCN: 759s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 759s Heterozygous SNPs with non-DH to resample for TCN: 759s int(0) 759s Loci to resample for TCN: 759s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 759s Identify loci used to bootstrap TCN means...done 759s Number of (#hets, #homs, #nonSNPs): (1311,0,3080) 759s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 759s Number of bootstrap samples: 100 759s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 759s Segment #3 (chr 1, tcnId=3, dhId=1) of 3...done 759s Bootstrapped segment mean levels 759s num [1:3, 1:100, 1:4] 1.38 2.08 2.63 1.38 2.07 ... 759s - attr(*, "dimnames")=List of 3 759s ..$ : NULL 759s ..$ : NULL 759s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 759s Calculating (C1,C2) mean levels from (TCN,DH) mean levels... 759s num [1:3, 1:100, 1:4] 1.38 2.08 2.63 1.38 2.07 ... 759s - attr(*, "dimnames")=List of 3 759s ..$ : NULL 759s ..$ : NULL 759s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 759s Calculating (C1,C2) mean levels from (TCN,DH) mean levels...done 759s Calculating polar (alpha,radius,manhattan) for change points... 759s num [1:2, 1:100, 1:2] -0.5588 -0.0962 -0.5365 -0.1285 -0.5378 ... 759s - attr(*, "dimnames")=List of 3 759s ..$ : NULL 759s ..$ : NULL 759s ..$ : chr [1:2] "c1" "c2" 759s Bootstrapped change points 759s num [1:2, 1:100, 1:5] -2.89 -1.78 -2.87 -1.86 -2.88 ... 759s - attr(*, "dimnames")=List of 3 759s ..$ : NULL 759s ..$ : NULL 759s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 759s Calculating polar (alpha,radius,manhattan) for change points...done 759s Bootstrapping (TCN,DH,C1,C2) segment mean levels...done 759s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data... 759s num [1:3, 1:4, 1:4] NA NA NA NA NA NA NA NA NA NA ... 759s - attr(*, "dimnames")=List of 3 759s ..$ : NULL 759s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 759s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 759s Field #1 ('tcn') of 4... 759s Segment #1 of 3... 759s Segment #1 of 3...done 759s Segment #2 of 3... 759s Segment #2 of 3...done 759s Segment #3 of 3... 759s Segment #3 of 3...done 759s Field #1 ('tcn') of 4...done 759s Field #2 ('dh') of 4... 759s Segment #1 of 3... 759s Segment #1 of 3...done 759s Segment #2 of 3... 759s Segment #2 of 3...done 759s Segment #3 of 3... 759s Segment #3 of 3...done 759s Field #2 ('dh') of 4...done 759s Field #3 ('c1') of 4... 759s Segment #1 of 3... 759s Segment #1 of 3...done 759s Segment #2 of 3... 759s Segment #2 of 3...done 759s Segment #3 of 3... 759s Segment #3 of 3...done 759s Field #3 ('c1') of 4...done 759s Field #4 ('c2') of 4... 759s Segment #1 of 3... 759s Segment #1 of 3...done 759s Segment #2 of 3... 759s Segment #2 of 3...done 759s Segment #3 of 3... 759s Segment #3 of 3...done 759s Field #4 ('c2') of 4...done 759s Bootstrap statistics 759s num [1:3, 1:4, 1:4] 1.38 2.06 2.62 1.38 2.06 ... 759s - attr(*, "dimnames")=List of 3 759s ..$ : NULL 759s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 759s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 759s Statistical sanity checks (iff B >= 100)... 759s Available summaries: 2.5%, 5%, 95%, 97.5% 759s Available quantiles: 0.025, 0.05, 0.95, 0.975 759s num [1:3, 1:4, 1:4] 1.38 2.06 2.62 1.38 2.06 ... 759s - attr(*, "dimnames")=List of 3 759s ..$ : NULL 759s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 759s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 759s Field #1 ('tcn') of 4... 759s Seg 1. mean=1.3859, range=[1.38092,1.3949], n=7599 759s Seg 2. mean=2.0704, range=[2.05747,2.08326], n=2668 759s Seg 3. mean=2.6341, range=[2.62068,2.64694], n=4391 759s Field #1 ('tcn') of 4...done 759s Field #2 ('dh') of 4... 759s Seg 1. mean=0.5237, range=[0.51753,0.532002], n=2111 759s Seg 2. mean=0.1542, range=[0.144468,0.16453], n=774 759s Seg 3. mean=0.2512, range=[0.242575,0.258832], n=1311 759s Field #2 ('dh') of 4...done 759s Field #3 ('c1') of 4... 759s Seg 1. mean=0.330052, range=[0.323996,0.336038], n=2111 759s Seg 2. mean=0.875572, range=[0.86318,0.887699], n=774 759s Seg 3. mean=0.986207, range=[0.975123,0.998982], n=1311 759s Field #3 ('c1') of 4...done 759s Field #4 ('c2') of 4... 759s Seg 1. mean=1.05585, range=[1.05006,1.06231], n=2111 759s Seg 2. mean=1.19483, range=[1.18417,1.2081], n=774 759s Seg 3. mean=1.64789, range=[1.63403,1.66098], n=1311 759s Field #4 ('c2') of 4...done 759s Statistical sanity checks (iff B >= 100)...done 759s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data...done 759s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data... 759s num [1:2, 1:4, 1:5] NA NA NA NA NA NA NA NA NA NA ... 759s - attr(*, "dimnames")=List of 3 759s ..$ : NULL 759s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 759s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 759s Field #1 ('alpha') of 5... 759s Changepoint #1 of 2... 759s Changepoint #1 of 2...done 759s Changepoint #2 of 2... 759s Changepoint #2 of 2...done 759s Field #1 ('alpha') of 5...done 759s Field #2 ('radius') of 5... 759s Changepoint #1 of 2... 759s Changepoint #1 of 2...done 759s Changepoint #2 of 2... 759s Changepoint #2 of 2...done 759s Field #2 ('radius') of 5...done 759s Field #3 ('manhattan') of 5... 759s Changepoint #1 of 2... 759s Changepoint #1 of 2...done 759s Changepoint #2 of 2... 759s Changepoint #2 of 2...done 759s Field #3 ('manhattan') of 5...done 759s Field #4 ('d1') of 5... 759s Changepoint #1 of 2... 759s Changepoint #1 of 2...done 759s Changepoint #2 of 2... 759s Changepoint #2 of 2...done 759s Field #4 ('d1') of 5...done 759s Field #5 ('d2') of 5... 759s Changepoint #1 of 2... 759s Changepoint #1 of 2...done 759s Changepoint #2 of 2... 759s Changepoint #2 of 2...done 759s Field #5 ('d2') of 5...done 759s Bootstrap statistics 759s num [1:2, 1:4, 1:5] -2.92 -1.86 -2.91 -1.85 -2.87 ... 759s - attr(*, "dimnames")=List of 3 759s ..$ : NULL 759s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 759s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 759s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data...done 759s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint...done 759s > print(fit) 759s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 759s 1 1 1 1 554484 143926517 7599 1.3859 2111 759s 2 1 2 1 143926517 185449813 2668 2.0704 774 759s 3 1 3 1 185449813 247137334 4391 2.6341 1311 759s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 759s 1 2111 2111 0.5237 0.3300521 1.055848 759s 2 774 774 0.1542 0.8755722 1.194828 759s 3 1311 1311 0.2512 0.9862070 1.647893 759s > plotTracks(fit) 759s > 759s > 759s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 759s > # Calling segments in allelic balance (AB) and 759s > # in loss-of-heterozygosity (LOH) 759s > # NOTE: Ideally, this should be done on whole-genome data 759s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 759s > fit <- callAB(fit, verbose=-10) 759s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 759s delta (offset adjusting for bias in DH): 0.3466649145302 759s alpha (CI quantile; significance level): 0.05 759s Calling segments... 759s Number of segments called allelic balance (AB): 2 (66.67%) of 3 759s Calling segments...done 759s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 759s > fit <- callLOH(fit, verbose=-10) 759s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 759s delta (offset adjusting for bias in C1): 0.771236438183453 759s alpha (CI quantile; significance level): 0.05 759s Calling segments... 759s Number of segments called low C1 (LowC1, "LOH_C1"): 1 (33.33%) of 3 759s Calling segments...done 759s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 759s > print(fit) 759s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 759s 1 1 1 1 554484 143926517 7599 1.3859 2111 759s 2 1 2 1 143926517 185449813 2668 2.0704 774 759s 3 1 3 1 185449813 247137334 4391 2.6341 1311 759s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean abCall lohCall 759s 1 2111 2111 0.5237 0.3300521 1.055848 FALSE TRUE 759s 2 774 774 0.1542 0.8755722 1.194828 TRUE FALSE 759s 3 1311 1311 0.2512 0.9862070 1.647893 TRUE FALSE 759s > plotTracks(fit) 759s > 759s > proc.time() 759s user system elapsed 759s 16.445 0.897 17.362 759s Test segmentByPairedPSCBS,noNormalBAFs passed 759s 0 759s Begin test segmentByPairedPSCBS,report 763s + cat segmentByPairedPSCBS,report.Rout 763s 763s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 763s Copyright (C) 2024 The R Foundation for Statistical Computing 763s Platform: aarch64-unknown-linux-gnu (64-bit) 763s 763s R is free software and comes with ABSOLUTELY NO WARRANTY. 763s You are welcome to redistribute it under certain conditions. 763s Type 'license()' or 'licence()' for distribution details. 763s 763s R is a collaborative project with many contributors. 763s Type 'contributors()' for more information and 763s 'citation()' on how to cite R or R packages in publications. 763s 763s Type 'demo()' for some demos, 'help()' for on-line help, or 763s 'help.start()' for an HTML browser interface to help. 763s Type 'q()' to quit R. 763s 763s [Previously saved workspace restored] 763s 763s > # This test script calls a report generator which requires 763s > # the 'ggplot2' package, which in turn will require packages 763s > # 'colorspace', 'dichromat', 'munsell', 'reshape2' and 'scales'. 763s > 763s > # Only run this test in full testing mode 763s > if (Sys.getenv("_R_CHECK_FULL_") != "") { 763s + library("PSCBS") 763s + 763s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 763s + # Load SNP microarray data 763s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 763s + data <- PSCBS::exampleData("paired.chr01") 763s + str(data) 763s + 763s + 763s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 763s + # Paired PSCBS segmentation 763s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 763s + # Drop single-locus outliers 763s + dataS <- dropSegmentationOutliers(data) 763s + 763s + # Speed up example by segmenting fewer loci 763s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 763s + 763s + str(dataS) 763s + 763s + gaps <- findLargeGaps(dataS, minLength=2e6) 763s + knownSegments <- gapsToSegments(gaps) 763s + 763s + # Paired PSCBS segmentation 763s + fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 763s + seed=0xBEEF, verbose=-10) 763s + 763s + # Fake a multi-chromosome segmentation 763s + fit1 <- fit 763s + fit2 <- renameChromosomes(fit, from=1, to=2) 763s + fit <- c(fit1, fit2) 763s + 763s + report(fit, sampleName="PairedPSCBS", studyName="PSCBS-Ex", verbose=-10) 763s + 763s + } # if (Sys.getenv("_R_CHECK_FULL_")) 763s > 763s > proc.time() 763s user system elapsed 763s 1.700 0.389 2.021 763s Test segmentByPairedPSCBS,report passed 763s + [ 0 != 0 ] 763s + echo Test segmentByPairedPSCBS,report passed 763s 0 763s Begin test segmentByPairedPSCBS,seqOfSegmentsByDP 763s + echo 0 763s + echo Begin test segmentByPairedPSCBS,seqOfSegmentsByDP 763s + exitcode=0 763s + R CMD BATCH segmentByPairedPSCBS,seqOfSegmentsByDP.R 799s + 799s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 799s Copyright (C) 2024 The R Foundation for Statistical Computing 799s Platform: aarch64-unknown-linux-gnu (64-bit) 799s 799s R is free software and comes with ABSOLUTELY NO WARRANTY. 799s You are welcome to redistribute it under certain conditions. 799s Type 'license()' or 'licence()' for distribution details. 799s 799s R is a collaborative project with many contributors. 799s Type 'contributors()' for more information and 799s 'citation()' on how to cite R or R packages in publications. 799s 799s Type 'demo()' for some demos, 'help()' for on-line help, or 799s 'help.start()' for an HTML browser interface to help. 799s Type 'q()' to quit R. 799s 799s [Previously saved workspace restored] 799s 799s > library("PSCBS") 799s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 799s 799s Attaching package: 'PSCBS' 799s 799s The following objects are masked from 'package:base': 799s 799s append, load 799s 799s > subplots <- R.utils::subplots 799s > stext <- R.utils::stext 799s > 799s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 799s > # Load SNP microarray data 799s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 799s > data <- PSCBS::exampleData("paired.chr01") 799s > str(data) 799s 'data.frame': 73346 obs. of 6 variables: 799s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 799s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 799s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 799s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 799s $ CN : num 2.36 2.13 2.59 1.93 1.71 ... 799s $ betaN : num 0.827 0.875 0.887 0.884 0.103 ... 799s > 799s > 799s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 799s > # Paired PSCBS segmentation 799s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 799s > # Drop single-locus outliers 799s > dataS <- dropSegmentationOutliers(data) 799s > 799s > # Run light-weight tests by default 799s > if (Sys.getenv("_R_CHECK_FULL_") == "") { 799s + # Use only every 5th data point 799s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 799s + # Number of segments (for assertion) 799s + nSegs <- 3L 799s + # Number of bootstrap samples (see below) 799s + B <- 100L 799s + } else { 799s + # Full tests 799s + nSegs <- 12L 799s + B <- 1000L 799s + } 799s > 799s > str(dataS) 799s 'data.frame': 14670 obs. of 6 variables: 799s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 799s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 799s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 799s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 799s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 799s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 799s > 799s > R.oo::attachLocally(dataS) 799s > 799s > 799s > gaps <- findLargeGaps(dataS, minLength=2e6) 799s > knownSegments <- gapsToSegments(gaps, dropGaps=TRUE) 799s > 799s > # Paired PSCBS segmentation 799s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 799s + seed=0xBEEF, verbose=-10) 799s Segmenting paired tumor-normal signals using Paired PSCBS... 799s Calling genotypes from normal allele B fractions... 799s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 799s Called genotypes: 799s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 799s - attr(*, "modelFit")=List of 1 799s ..$ :List of 7 799s .. ..$ flavor : chr "density" 799s .. ..$ cn : int 2 799s .. ..$ nbrOfGenotypeGroups: int 3 799s .. ..$ tau : num [1:2] 0.315 0.677 799s .. ..$ n : int 14640 799s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 799s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 799s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 799s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 799s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 799s .. .. ..$ type : chr [1:2] "valley" "valley" 799s .. .. ..$ x : num [1:2] 0.315 0.677 799s .. .. ..$ density: num [1:2] 0.522 0.552 799s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 799s muN 799s 0 0.5 1 799s 5221 4198 5251 799s Calling genotypes from normal allele B fractions...done 799s Normalizing betaT using betaN (TumorBoost)... 799s Normalized BAFs: 799s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 799s - attr(*, "modelFit")=List of 5 799s ..$ method : chr "normalizeTumorBoost" 799s ..$ flavor : chr "v4" 799s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 799s .. ..- attr(*, "modelFit")=List of 1 799s .. .. ..$ :List of 7 799s .. .. .. ..$ flavor : chr "density" 799s .. .. .. ..$ cn : int 2 799s .. .. .. ..$ nbrOfGenotypeGroups: int 3 799s .. .. .. ..$ tau : num [1:2] 0.315 0.677 799s .. .. .. ..$ n : int 14640 799s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 799s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 799s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 799s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 799s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 799s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 799s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 799s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 799s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 799s ..$ preserveScale: logi FALSE 799s ..$ scaleFactor : num NA 799s Normalizing betaT using betaN (TumorBoost)...done 799s Setup up data... 799s 'data.frame': 14670 obs. of 7 variables: 799s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 799s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 799s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 799s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 799s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 799s ..- attr(*, "modelFit")=List of 5 799s .. ..$ method : chr "normalizeTumorBoost" 799s .. ..$ flavor : chr "v4" 799s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 799s .. .. ..- attr(*, "modelFit")=List of 1 799s .. .. .. ..$ :List of 7 799s .. .. .. .. ..$ flavor : chr "density" 799s .. .. .. .. ..$ cn : int 2 799s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 799s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 799s .. .. .. .. ..$ n : int 14640 799s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 799s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 799s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 799s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 799s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 799s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 799s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 799s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 799s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 799s .. ..$ preserveScale: logi FALSE 799s .. ..$ scaleFactor : num NA 799s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 799s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 799s ..- attr(*, "modelFit")=List of 1 799s .. ..$ :List of 7 799s .. .. ..$ flavor : chr "density" 799s .. .. ..$ cn : int 2 799s .. .. ..$ nbrOfGenotypeGroups: int 3 799s .. .. ..$ tau : num [1:2] 0.315 0.677 799s .. .. ..$ n : int 14640 799s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 799s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 799s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 799s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 799s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 799s .. .. .. ..$ type : chr [1:2] "valley" "valley" 799s .. .. .. ..$ x : num [1:2] 0.315 0.677 799s .. .. .. ..$ density: num [1:2] 0.522 0.552 799s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 799s Setup up data...done 799s Dropping loci for which TCNs are missing... 799s Number of loci dropped: 12 799s Dropping loci for which TCNs are missing...done 799s Ordering data along genome... 799s 'data.frame': 14658 obs. of 7 variables: 799s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 799s $ x : num 554484 730720 782343 878522 916294 ... 799s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 799s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 799s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 799s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 799s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 799s Ordering data along genome...done 799s Keeping only current chromosome for 'knownSegments'... 799s Chromosome: 1 799s Known segments for this chromosome: 799s chromosome start end length 799s 1 1 -Inf 120908858 Inf 799s 2 1 142693888 Inf Inf 799s Keeping only current chromosome for 'knownSegments'...done 799s alphaTCN: 0.009 799s alphaDH: 0.001 799s Number of loci: 14658 799s Calculating DHs... 799s Number of SNPs: 14658 799s Number of heterozygous SNPs: 4196 (28.63%) 799s Normalized DHs: 799s num [1:14658] NA NA NA NA NA ... 799s Calculating DHs...done 799s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 799s Produced 2 seeds from this stream for future usage 799s Identification of change points by total copy numbers... 799s Segmenting by CBS... 799s Chromosome: 1 799s Segmenting multiple segments on current chromosome... 799s Number of segments: 2 799s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 799s Produced 2 seeds from this stream for future usage 799s Segmenting by CBS... 799s Chromosome: 1 799s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 799s Segmenting by CBS...done 799s Segmenting by CBS... 799s Chromosome: 1 799s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 799s Segmenting by CBS...done 799s Segmenting multiple segments on current chromosome...done 799s Segmenting by CBS...done 799s List of 4 799s $ data :'data.frame': 14658 obs. of 4 variables: 799s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 799s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 799s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 799s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 799s $ output :'data.frame': 3 obs. of 6 variables: 799s ..$ sampleName: chr [1:3] NA NA NA 799s ..$ chromosome: int [1:3] 1 1 1 799s ..$ start : num [1:3] 5.54e+05 1.43e+08 1.85e+08 799s ..$ end : num [1:3] 1.21e+08 1.85e+08 2.47e+08 799s ..$ nbrOfLoci : int [1:3] 7586 2681 4391 799s ..$ mean : num [1:3] 1.39 2.07 2.63 799s $ segRows:'data.frame': 3 obs. of 2 variables: 799s ..$ startRow: int [1:3] 1 7587 10268 799s ..$ endRow : int [1:3] 7586 10267 14658 799s $ params :List of 5 799s ..$ alpha : num 0.009 799s ..$ undo : num 0 799s ..$ joinSegments : logi TRUE 799s ..$ knownSegments:'data.frame': 2 obs. of 3 variables: 799s .. ..$ chromosome: int [1:2] 1 1 799s .. ..$ start : num [1:2] -Inf 1.43e+08 799s .. ..$ end : num [1:2] 1.21e+08 Inf 799s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 799s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 799s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.444 0 0.444 0 0 799s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 799s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 799s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 799s Identification of change points by total copy numbers...done 799s Restructure TCN segmentation results... 799s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 799s 1 1 554484 120908858 7586 1.3853 799s 2 1 142693888 185449813 2681 2.0689 799s 3 1 185449813 247137334 4391 2.6341 799s Number of TCN segments: 3 799s Restructure TCN segmentation results...done 799s Total CN segment #1 ([ 554484,1.20909e+08]) of 3... 799s Number of TCN loci in segment: 7586 799s Locus data for TCN segment: 799s 'data.frame': 7586 obs. of 9 variables: 799s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 799s $ x : num 554484 730720 782343 878522 916294 ... 799s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 799s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 799s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 799s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 799s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 799s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 799s $ rho : num NA NA NA NA NA ... 799s Number of loci: 7586 799s Number of SNPs: 2108 (27.79%) 799s Number of heterozygous SNPs: 2108 (100.00%) 799s Chromosome: 1 799s Segmenting DH signals... 799s Segmenting by CBS... 799s Chromosome: 1 799s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 799s Segmenting by CBS...done 799s List of 4 799s $ data :'data.frame': 7586 obs. of 4 variables: 799s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 799s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 799s ..$ y : num [1:7586] NA NA NA NA NA ... 799s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 799s $ output :'data.frame': 1 obs. of 6 variables: 799s ..$ sampleName: chr NA 799s ..$ chromosome: int 1 799s ..$ start : num 554484 799s ..$ end : num 1.21e+08 799s ..$ nbrOfLoci : int 2108 799s ..$ mean : num 0.512 799s $ segRows:'data.frame': 1 obs. of 2 variables: 799s ..$ startRow: int 10 799s ..$ endRow : int 7574 799s $ params :List of 5 799s ..$ alpha : num 0.001 799s ..$ undo : num 0 799s ..$ joinSegments : logi TRUE 799s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 799s .. ..$ chromosome: int 1 799s .. ..$ start : num 554484 799s .. ..$ end : num 1.21e+08 799s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 799s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 799s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.23 0.002 0.233 0 0 799s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 799s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 799s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 799s DH segmentation (locally-indexed) rows: 799s startRow endRow 799s 1 10 7574 799s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 799s DH segmentation rows: 799s startRow endRow 799s 1 10 7574 799s Segmenting DH signals...done 799s DH segmentation table: 799s dhStart dhEnd dhNbrOfLoci dhMean 799s 1 554484 120908858 2108 0.5116 799s startRow endRow 799s 1 10 7574 799s Rows: 799s [1] 1 799s TCN segmentation rows: 799s startRow endRow 799s 1 1 7586 799s TCN and DH segmentation rows: 799s startRow endRow 799s 1 1 7586 799s startRow endRow 799s 1 10 7574 799s NULL 799s TCN segmentation (expanded) rows: 799s startRow endRow 799s 1 1 7586 799s TCN and DH segmentation rows: 799s startRow endRow 799s 1 1 7586 799s 2 7587 10267 799s 3 10268 14658 799s startRow endRow 799s 1 10 7574 799s startRow endRow 799s 1 1 7586 799s Total CN segmentation table (expanded): 799s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 799s 1 1 554484 120908858 7586 1.3853 2108 2108 799s (TCN,DH) segmentation for one total CN segment: 799s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 799s 1 1 1 1 554484 120908858 7586 1.3853 2108 799s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 799s 1 2108 554484 120908858 2108 0.5116 799s Total CN segment #1 ([ 554484,1.20909e+08]) of 3...done 799s Total CN segment #2 ([1.42694e+08,1.8545e+08]) of 3... 799s Number of TCN loci in segment: 2681 799s Locus data for TCN segment: 799s 'data.frame': 2681 obs. of 9 variables: 799s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 799s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 799s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 799s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 799s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 799s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 799s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 799s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 799s $ rho : num 0.117 0.258 NA NA NA ... 799s Number of loci: 2681 799s Number of SNPs: 777 (28.98%) 799s Number of heterozygous SNPs: 777 (100.00%) 799s Chromosome: 1 799s Segmenting DH signals... 799s Segmenting by CBS... 799s Chromosome: 1 799s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 799s Segmenting by CBS...done 799s List of 4 799s $ data :'data.frame': 2681 obs. of 4 variables: 799s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 799s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 799s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 799s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 799s $ output :'data.frame': 1 obs. of 6 variables: 799s ..$ sampleName: chr NA 799s ..$ chromosome: int 1 799s ..$ start : num 1.43e+08 799s ..$ end : num 1.85e+08 799s ..$ nbrOfLoci : int 777 799s ..$ mean : num 0.0973 799s $ segRows:'data.frame': 1 obs. of 2 variables: 799s ..$ startRow: int 1 799s ..$ endRow : int 2677 799s $ params :List of 5 799s ..$ alpha : num 0.001 799s ..$ undo : num 0 799s ..$ joinSegments : logi TRUE 799s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 799s .. ..$ chromosome: int 1 799s .. ..$ start : num 1.43e+08 799s .. ..$ end : num 1.85e+08 799s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 799s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 799s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.028 0 0.028 0 0 799s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 799s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 799s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 799s DH segmentation (locally-indexed) rows: 799s startRow endRow 799s 1 1 2677 799s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 799s DH segmentation rows: 799s startRow endRow 799s 1 7587 10263 799s Segmenting DH signals...done 799s DH segmentation table: 799s dhStart dhEnd dhNbrOfLoci dhMean 799s 1 142693888 185449813 777 0.0973 799s startRow endRow 799s 1 7587 10263 799s Rows: 799s [1] 2 799s TCN segmentation rows: 799s startRow endRow 799s 2 7587 10267 799s TCN and DH segmentation rows: 799s startRow endRow 799s 2 7587 10267 799s startRow endRow 799s 1 7587 10263 799s startRow endRow 799s 1 1 7586 799s TCN segmentation (expanded) rows: 799s startRow endRow 799s 1 1 7586 799s 2 7587 10267 799s TCN and DH segmentation rows: 799s startRow endRow 799s 1 1 7586 799s 2 7587 10267 799s 3 10268 14658 799s startRow endRow 799s 1 10 7574 799s 2 7587 10263 799s startRow endRow 799s 1 1 7586 799s 2 7587 10267 799s Total CN segmentation table (expanded): 799s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 799s 2 1 142693888 185449813 2681 2.0689 777 777 799s (TCN,DH) segmentation for one total CN segment: 799s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 799s 2 2 1 1 142693888 185449813 2681 2.0689 777 799s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 799s 2 777 142693888 185449813 777 0.0973 799s Total CN segment #2 ([1.42694e+08,1.8545e+08]) of 3...done 799s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 799s Number of TCN loci in segment: 4391 799s Locus data for TCN segment: 799s 'data.frame': 4391 obs. of 9 variables: 799s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 799s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 799s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 799s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 799s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 799s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 799s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 799s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 799s $ rho : num NA 0.2186 NA 0.0503 NA ... 799s Number of loci: 4391 799s Number of SNPs: 1311 (29.86%) 799s Number of heterozygous SNPs: 1311 (100.00%) 799s Chromosome: 1 799s Segmenting DH signals... 799s Segmenting by CBS... 799s Chromosome: 1 799s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 799s Segmenting by CBS...done 799s List of 4 799s $ data :'data.frame': 4391 obs. of 4 variables: 799s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 799s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 799s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 799s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 799s $ output :'data.frame': 1 obs. of 6 variables: 799s ..$ sampleName: chr NA 799s ..$ chromosome: int 1 799s ..$ start : num 1.85e+08 799s ..$ end : num 2.47e+08 799s ..$ nbrOfLoci : int 1311 799s ..$ mean : num 0.23 799s $ segRows:'data.frame': 1 obs. of 2 variables: 799s ..$ startRow: int 2 799s ..$ endRow : int 4388 799s $ params :List of 5 799s ..$ alpha : num 0.001 799s ..$ undo : num 0 799s ..$ joinSegments : logi TRUE 799s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 799s .. ..$ chromosome: int 1 799s .. ..$ start : num 1.85e+08 799s .. ..$ end : num 2.47e+08 799s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 799s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 799s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.1 0.001 0.102 0 0 799s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 799s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 799s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 799s DH segmentation (locally-indexed) rows: 799s startRow endRow 799s 1 2 4388 799s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 799s DH segmentation rows: 799s startRow endRow 799s 1 10269 14655 799s Segmenting DH signals...done 799s DH segmentation table: 799s dhStart dhEnd dhNbrOfLoci dhMean 799s 1 185449813 247137334 1311 0.2295 799s startRow endRow 799s 1 10269 14655 799s Rows: 799s [1] 3 799s TCN segmentation rows: 799s startRow endRow 799s 3 10268 14658 799s TCN and DH segmentation rows: 799s startRow endRow 799s 3 10268 14658 799s startRow endRow 799s 1 10269 14655 799s startRow endRow 799s 1 1 7586 799s 2 7587 10267 799s TCN segmentation (expanded) rows: 799s startRow endRow 799s 1 1 7586 799s 2 7587 10267 799s 3 10268 14658 799s TCN and DH segmentation rows: 799s startRow endRow 799s 1 1 7586 799s 2 7587 10267 799s 3 10268 14658 799s startRow endRow 799s 1 10 7574 799s 2 7587 10263 799s 3 10269 14655 799s startRow endRow 799s 1 1 7586 799s 2 7587 10267 799s 3 10268 14658 799s Total CN segmentation table (expanded): 799s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 799s 3 1 185449813 247137334 4391 2.6341 1311 1311 799s (TCN,DH) segmentation for one total CN segment: 799s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 799s 3 3 1 1 185449813 247137334 4391 2.6341 1311 799s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 799s 3 1311 185449813 247137334 1311 0.2295 799s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 799s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 799s 1 1 1 1 554484 120908858 7586 1.3853 2108 799s 2 1 2 1 142693888 185449813 2681 2.0689 777 799s 3 1 3 1 185449813 247137334 4391 2.6341 1311 799s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 799s 1 2108 554484 120908858 2108 0.5116 799s 2 777 142693888 185449813 777 0.0973 799s 3 1311 185449813 247137334 1311 0.2295 799s Calculating (C1,C2) per segment... 799s Calculating (C1,C2) per segment...done 799s Number of segments: 3 799s Segmenting paired tumor-normal signals using Paired PSCBS...done 799s Post-segmenting TCNs... 799s Number of segments: 3 799s Number of chromosomes: 1 799s [1] 1 799s Chromosome 1 ('chr01') of 1... 799s Rows: 799s [1] 1 2 3 799s Number of segments: 3 799s TCN segment #1 ('1') of 3... 799s Nothing todo. Only one DH segmentation. Skipping. 799s TCN segment #1 ('1') of 3...done 799s TCN segment #2 ('2') of 3... 799s Nothing todo. Only one DH segmentation. Skipping. 799s TCN segment #2 ('2') of 3...done 799s TCN segment #3 ('3') of 3... 799s Nothing todo. Only one DH segmentation. Skipping. 799s TCN segment #3 ('3') of 3...done 799s Chromosome 1 ('chr01') of 1...done 799s Update (C1,C2) per segment... 799s Update (C1,C2) per segment...done 799s Post-segmenting TCNs...done 799s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 799s 1 1 1 1 554484 120908858 7586 1.3853 2108 799s 2 1 2 1 142693888 185449813 2681 2.0689 777 799s 3 1 3 1 185449813 247137334 4391 2.6341 1311 799s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 799s 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 799s 2 777 142693888 185449813 777 0.0973 0.9337980 1.135102 799s 3 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 799s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 799s 1 1 1 1 554484 120908858 7586 1.3853 2108 799s 2 1 2 1 142693888 185449813 2681 2.0689 777 799s 3 1 3 1 185449813 247137334 4391 2.6341 1311 799s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 799s 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 799s 2 777 142693888 185449813 777 0.0973 0.9337980 1.135102 799s 3 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 799s > print(fit) 799s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 799s 1 1 1 1 554484 120908858 7586 1.3853 2108 799s 2 1 2 1 142693888 185449813 2681 2.0689 777 799s 3 1 3 1 185449813 247137334 4391 2.6341 1311 799s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 799s 1 2108 2108 0.5116 0.3382903 1.047010 799s 2 777 777 0.0973 0.9337980 1.135102 799s 3 1311 1311 0.2295 1.0147870 1.619313 799s > 799s > fit1 <- fit 799s > fit2 <- renameChromosomes(fit1, from=1, to=2) 799s > fit <- c(fit1, fit2) 799s > knownSegments <- tileChromosomes(fit)$params$knownSegments 799s > 799s > segList <- seqOfSegmentsByDP(fit, verbose=-10) 799s Identifying optimal sets of segments via dynamic programming... 799s Shifting TCN levels for every second segment... 799s Split up into non-empty independent regions... 799s Chromosome #1 ('1') of 2... 799s Number of loci on chromosome: 14658 799s Known segments on chromosome: 799s chromosome start end 799s 1 1 -Inf 120908858 799s 2 1 142693888 Inf 799s Known segment #1 of 2... 799s chromosome start end 799s 1 1 -Inf 120908858 799s Known segment #1 of 2...done 799s Known segment #2 of 2... 799s chromosome start end 799s 2 1 142693888 Inf 799s Known segment #2 of 2...done 799s Chromosome #1 ('1') of 2...done 799s Chromosome #2 ('2') of 2... 799s Number of loci on chromosome: 14658 799s Known segments on chromosome: 799s chromosome start end 799s 3 2 -Inf 120908858 799s 4 2 142693888 Inf 799s Known segment #1 of 2... 799s chromosome start end 799s 3 2 -Inf 120908858 799s Known segment #1 of 2...done 799s Known segment #2 of 2... 799s chromosome start end 799s 4 2 142693888 Inf 799s Known segment #2 of 2...done 799s Chromosome #2 ('2') of 2...done 799s Number of independent non-empty regions: 4 799s Split up into non-empty independent regions...done 799s Shift every other region... 799s Shift every other region...done 799s Merge... 799s Merge...done 799s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 799s 1 1 1 1 554484 120908858 7586 101.3853 2108 799s 2 1 2 1 142693888 185449813 2681 2.0689 777 799s 3 1 3 1 185449813 247137334 4391 2.6341 1311 799s 4 2 1 1 554484 120908858 7586 101.3853 2108 799s 5 2 2 1 142693888 185449813 2681 2.0689 777 799s 6 2 3 1 185449813 247137334 4391 2.6341 1311 799s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 799s 1 2108 554484 120908858 2108 0.511612 24.757671 76.627587 799s 2 777 142693888 185449813 777 0.097300 0.933798 1.135102 799s 3 1311 185449813 247137334 1311 0.229500 1.014787 1.619313 799s 4 2108 554484 120908858 2108 0.511612 24.757671 76.627587 799s 5 777 142693888 185449813 777 0.097300 0.933798 1.135102 799s 6 1311 185449813 247137334 1311 0.229500 1.014787 1.619313 799s Shifting TCN levels for every second segment...done 799s Extracting signals for dynamic programming... 799s CT rho 799s Min. : 0.805 Min. :0.000 799s 1st Qu.: 2.407 1st Qu.:0.139 799s Median :100.927 Median :0.293 799s Mean : 53.638 Mean :0.347 799s 3rd Qu.:101.370 3rd Qu.:0.557 799s Max. :103.080 Max. :1.022 799s NA's :20924 799s Extracting signals for dynamic programming...done 799s Dynamic programming... 799s Number of "DP" change points: 5 799s int [1:5] 7586 10267 14658 22244 24925 799s List of 4 799s $ jump :List of 5 799s ..$ : num 22244 799s ..$ : num [1:2] 7586 14658 799s ..$ : num [1:3] 7586 14658 22244 799s ..$ : num [1:4] 7586 10267 14658 22244 799s ..$ : num [1:5] 7586 10267 14658 22244 24925 799s $ rse : num [1:6] 71699116 47249179 35852530 5945 5410 ... 799s $ kbest: num 4 799s $ V : num [1:6, 1:6] 1114 0 0 0 0 ... 799s Dynamic programming...done 799s Excluding cases where known segments no longer correct... 799s Number of independent non-empty regions: 4 799s List of 3 799s $ : num [1:3] 7586 14658 22244 799s $ : num [1:4] 7586 10267 14658 22244 799s $ : num [1:5] 7586 10267 14658 22244 24925 799s Excluding cases where known segments no longer correct...done 799s List of 3 799s $ :'data.frame': 4 obs. of 3 variables: 799s ..$ chromosome: int [1:4] 1 1 2 2 799s ..$ start : num [1:4] 5.54e+05 1.43e+08 5.54e+05 1.43e+08 799s ..$ end : num [1:4] 1.21e+08 2.47e+08 1.21e+08 2.47e+08 799s $ :'data.frame': 5 obs. of 3 variables: 799s ..$ chromosome: int [1:5] 1 1 1 2 2 799s ..$ start : num [1:5] 5.54e+05 1.43e+08 1.85e+08 5.54e+05 1.43e+08 799s ..$ end : num [1:5] 1.21e+08 1.85e+08 2.47e+08 1.21e+08 2.47e+08 799s $ :'data.frame': 6 obs. of 3 variables: 799s ..$ chromosome: int [1:6] 1 1 1 2 2 2 799s ..$ start : num [1:6] 5.54e+05 1.43e+08 1.85e+08 5.54e+05 1.43e+08 ... 799s ..$ end : num [1:6] 1.21e+08 1.85e+08 2.47e+08 1.21e+08 1.85e+08 ... 799s Sequence of number of "DP" change points: 799s [1] 3 4 5 799s Sequence of number of segments: 799s [1] 4 5 6 799s Sequence of number of "discovered" change points: 799s [1] 0 1 2 799s Identifying optimal sets of segments via dynamic programming...done 799s > K <- length(segList) 799s > ks <- seq(from=1, to=K, length.out=min(5,K)) 799s > subplots(length(ks), ncol=1, byrow=TRUE) 799s > par(mar=c(2,1,1,1)) 799s > for (kk in ks) { 799s + knownSegmentsKK <- segList[[kk]] 799s + fitKK <- resegment(fit, knownSegments=knownSegmentsKK, undoTCN=+Inf, undoDH=+Inf) 799s + plotTracks(fitKK, tracks="tcn,c1,c2", Clim=c(0,5), add=TRUE) 799s + abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 799s + stext(side=3, pos=0, sprintf("Number of segments: %d", nrow(knownSegmentsKK))) 799s + } # for (kk ...) 799s > 799s > proc.time() 799s user system elapsed 799s 30.583 1.108 31.719 799s Test segmentByPairedPSCBS,seqOfSegmentsByDP passed 799s 0 799s Begin test segmentByPairedPSCBS 799s cat segmentByPairedPSCBS,seqOfSegmentsByDP.Rout 799s + [ 0 != 0 ] 799s + echo Test segmentByPairedPSCBS,seqOfSegmentsByDP passed 799s + echo 0 799s + echo Begin test segmentByPairedPSCBS 799s + exitcode=0 799s + R CMD BATCH segmentByPairedPSCBS.R 841s + cat segmentByPairedPSCBS.Rout 841s 841s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 841s Copyright (C) 2024 The R Foundation for Statistical Computing 841s Platform: aarch64-unknown-linux-gnu (64-bit) 841s 841s R is free software and comes with ABSOLUTELY NO WARRANTY. 841s You are welcome to redistribute it under certain conditions. 841s Type 'license()' or 'licence()' for distribution details. 841s 841s R is a collaborative project with many contributors. 841s Type 'contributors()' for more information and 841s 'citation()' on how to cite R or R packages in publications. 841s 841s Type 'demo()' for some demos, 'help()' for on-line help, or 841s 'help.start()' for an HTML browser interface to help. 841s Type 'q()' to quit R. 841s 841s [Previously saved workspace restored] 841s 841s > ########################################################### 841s > # This tests: 841s > # - segmentByPairedPSCBS(...) 841s > # - segmentByPairedPSCBS(..., knownSegments) 841s > # - tileChromosomes() 841s > # - plotTracks() 841s > ########################################################### 841s > library("PSCBS") 841s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 841s 841s Attaching package: 'PSCBS' 841s 841s The following objects are masked from 'package:base': 841s 841s append, load 841s 841s > 841s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 841s > # Load SNP microarray data 841s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 841s > data <- PSCBS::exampleData("paired.chr01") 841s > 841s > 841s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 841s > # Paired PSCBS segmentation 841s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 841s > # Drop single-locus outliers 841s > dataS <- dropSegmentationOutliers(data) 841s > 841s > # Run light-weight tests by default 841s > if (Sys.getenv("_R_CHECK_FULL_") == "") { 841s + # Use only every 5th data point 841s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 841s + # Number of segments (for assertion) 841s + nSegs <- 4L 841s + } else { 841s + # Full tests 841s + nSegs <- 11L 841s + } 841s > 841s > str(dataS) 841s 'data.frame': 14670 obs. of 6 variables: 841s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 841s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 841s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 841s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 841s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 841s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 841s > 841s > fig <- 1 841s > 841s > 841s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 841s > # (a) Don't segment the centromere (and force a separator) 841s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 841s > knownSegments <- data.frame( 841s + chromosome = c( 1, 1, 1), 841s + start = c( -Inf, NA, 141510003), 841s + end = c(120992603, NA, +Inf) 841s + ) 841s > 841s > 841s > # Paired PSCBS segmentation 841s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 841s + seed=0xBEEF, verbose=-10) 841s Segmenting paired tumor-normal signals using Paired PSCBS... 841s Calling genotypes from normal allele B fractions... 841s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 841s Called genotypes: 841s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 841s - attr(*, "modelFit")=List of 1 841s ..$ :List of 7 841s .. ..$ flavor : chr "density" 841s .. ..$ cn : int 2 841s .. ..$ nbrOfGenotypeGroups: int 3 841s .. ..$ tau : num [1:2] 0.315 0.677 841s .. ..$ n : int 14640 841s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 841s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 841s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 841s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 841s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 841s .. .. ..$ type : chr [1:2] "valley" "valley" 841s .. .. ..$ x : num [1:2] 0.315 0.677 841s .. .. ..$ density: num [1:2] 0.522 0.552 841s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 841s muN 841s 0 0.5 1 841s 5221 4198 5251 841s Calling genotypes from normal allele B fractions...done 841s Normalizing betaT using betaN (TumorBoost)... 841s Normalized BAFs: 841s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 841s - attr(*, "modelFit")=List of 5 841s ..$ method : chr "normalizeTumorBoost" 841s ..$ flavor : chr "v4" 841s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 841s .. ..- attr(*, "modelFit")=List of 1 841s .. .. ..$ :List of 7 841s .. .. .. ..$ flavor : chr "density" 841s .. .. .. ..$ cn : int 2 841s .. .. .. ..$ nbrOfGenotypeGroups: int 3 841s .. .. .. ..$ tau : num [1:2] 0.315 0.677 841s .. .. .. ..$ n : int 14640 841s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 841s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 841s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 841s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 841s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 841s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 841s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 841s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 841s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 841s ..$ preserveScale: logi FALSE 841s ..$ scaleFactor : num NA 841s Normalizing betaT using betaN (TumorBoost)...done 841s Setup up data... 841s 'data.frame': 14670 obs. of 7 variables: 841s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 841s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 841s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 841s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 841s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 841s ..- attr(*, "modelFit")=List of 5 841s .. ..$ method : chr "normalizeTumorBoost" 841s .. ..$ flavor : chr "v4" 841s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 841s .. .. ..- attr(*, "modelFit")=List of 1 841s .. .. .. ..$ :List of 7 841s .. .. .. .. ..$ flavor : chr "density" 841s .. .. .. .. ..$ cn : int 2 841s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 841s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 841s .. .. .. .. ..$ n : int 14640 841s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 841s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 841s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 841s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 841s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 841s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 841s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 841s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 841s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 841s .. ..$ preserveScale: logi FALSE 841s .. ..$ scaleFactor : num NA 841s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 841s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 841s ..- attr(*, "modelFit")=List of 1 841s .. ..$ :List of 7 841s .. .. ..$ flavor : chr "density" 841s .. .. ..$ cn : int 2 841s .. .. ..$ nbrOfGenotypeGroups: int 3 841s .. .. ..$ tau : num [1:2] 0.315 0.677 841s .. .. ..$ n : int 14640 841s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 841s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 841s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 841s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 841s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 841s .. .. .. ..$ type : chr [1:2] "valley" "valley" 841s .. .. .. ..$ x : num [1:2] 0.315 0.677 841s .. .. .. ..$ density: num [1:2] 0.522 0.552 841s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 841s Setup up data...done 841s Dropping loci for which TCNs are missing... 841s Number of loci dropped: 12 841s Dropping loci for which TCNs are missing...done 841s Ordering data along genome... 841s 'data.frame': 14658 obs. of 7 variables: 841s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 841s $ x : num 554484 730720 782343 878522 916294 ... 841s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 841s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 841s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 841s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 841s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 841s Ordering data along genome...done 841s Keeping only current chromosome for 'knownSegments'... 841s Chromosome: 1 841s Known segments for this chromosome: 841s chromosome start end 841s 1 1 -Inf 120992603 841s 2 1 NA NA 841s 3 1 141510003 Inf 841s Keeping only current chromosome for 'knownSegments'...done 841s alphaTCN: 0.009 841s alphaDH: 0.001 841s Number of loci: 14658 841s Calculating DHs... 841s Number of SNPs: 14658 841s Number of heterozygous SNPs: 4196 (28.63%) 841s Normalized DHs: 841s num [1:14658] NA NA NA NA NA ... 841s Calculating DHs...done 841s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 841s Produced 2 seeds from this stream for future usage 841s Identification of change points by total copy numbers... 841s Segmenting by CBS... 841s Chromosome: 1 841s Segmenting multiple segments on current chromosome... 841s Number of segments: 3 841s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 841s Produced 3 seeds from this stream for future usage 841s Segmenting by CBS... 841s Chromosome: 1 841s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 841s Segmenting by CBS...done 841s Segmenting by CBS... 841s Chromosome: 1 841s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 841s Segmenting by CBS...done 841s Segmenting multiple segments on current chromosome...done 841s Segmenting by CBS...done 841s List of 4 841s $ data :'data.frame': 14658 obs. of 4 variables: 841s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 841s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 841s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 841s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 841s $ output :'data.frame': 4 obs. of 6 variables: 841s ..$ sampleName: chr [1:4] NA NA NA NA 841s ..$ chromosome: int [1:4] 1 NA 1 1 841s ..$ start : num [1:4] 5.54e+05 NA 1.42e+08 1.85e+08 841s ..$ end : num [1:4] 1.21e+08 NA 1.85e+08 2.47e+08 841s ..$ nbrOfLoci : int [1:4] 7586 NA 2681 4391 841s ..$ mean : num [1:4] 1.39 NA 2.07 2.63 841s $ segRows:'data.frame': 4 obs. of 2 variables: 841s ..$ startRow: int [1:4] 1 NA 7587 10268 841s ..$ endRow : int [1:4] 7586 NA 10267 14658 841s $ params :List of 5 841s ..$ alpha : num 0.009 841s ..$ undo : num 0 841s ..$ joinSegments : logi TRUE 841s ..$ knownSegments:'data.frame': 4 obs. of 3 variables: 841s .. ..$ chromosome: num [1:4] 1 1 2 1 841s .. ..$ start : num [1:4] -Inf -Inf -Inf 1.42e+08 841s .. ..$ end : num [1:4] 1.21e+08 Inf Inf Inf 841s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 841s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 841s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.812 0.015 0.828 0 0 841s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 841s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 841s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 841s Identification of change points by total copy numbers...done 841s Restructure TCN segmentation results... 841s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 841s 1 1 554484 120992603 7586 1.3853 841s 2 NA NA NA NA NA 841s 3 1 141510003 185449813 2681 2.0689 841s 4 1 185449813 247137334 4391 2.6341 841s Number of TCN segments: 4 841s Restructure TCN segmentation results...done 841s Total CN segment #1 ([ 554484,1.20993e+08]) of 4... 841s Number of TCN loci in segment: 7586 841s Locus data for TCN segment: 841s 'data.frame': 7586 obs. of 9 variables: 841s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 841s $ x : num 554484 730720 782343 878522 916294 ... 841s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 841s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 841s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 841s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 841s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 841s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 841s $ rho : num NA NA NA NA NA ... 841s Number of loci: 7586 841s Number of SNPs: 2108 (27.79%) 841s Number of heterozygous SNPs: 2108 (100.00%) 841s Chromosome: 1 841s Segmenting DH signals... 841s Segmenting by CBS... 841s Chromosome: 1 841s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 841s Segmenting by CBS...done 841s List of 4 841s $ data :'data.frame': 7586 obs. of 4 variables: 841s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 841s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 841s ..$ y : num [1:7586] NA NA NA NA NA ... 841s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 841s $ output :'data.frame': 1 obs. of 6 variables: 841s ..$ sampleName: chr NA 841s ..$ chromosome: int 1 841s ..$ start : num 554484 841s ..$ end : num 1.21e+08 841s ..$ nbrOfLoci : int 2108 841s ..$ mean : num 0.512 841s $ segRows:'data.frame': 1 obs. of 2 variables: 841s ..$ startRow: int 10 841s ..$ endRow : int 7574 841s $ params :List of 5 841s ..$ alpha : num 0.001 841s ..$ undo : num 0 841s ..$ joinSegments : logi TRUE 841s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 841s .. ..$ chromosome: int 1 841s .. ..$ start : num 554484 841s .. ..$ end : num 1.21e+08 841s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 841s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 841s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.195 0 0.196 0 0 841s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 841s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 841s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 841s DH segmentation (locally-indexed) rows: 841s startRow endRow 841s 1 10 7574 841s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 841s DH segmentation rows: 841s startRow endRow 841s 1 10 7574 841s Segmenting DH signals...done 841s DH segmentation table: 841s dhStart dhEnd dhNbrOfLoci dhMean 841s 1 554484 120992603 2108 0.5116 841s startRow endRow 841s 1 10 7574 841s Rows: 841s [1] 1 841s TCN segmentation rows: 841s startRow endRow 841s 1 1 7586 841s TCN and DH segmentation rows: 841s startRow endRow 841s 1 1 7586 841s startRow endRow 841s 1 10 7574 841s NULL 841s TCN segmentation (expanded) rows: 841s startRow endRow 841s 1 1 7586 841s TCN and DH segmentation rows: 841s startRow endRow 841s 1 1 7586 841s 2 NA NA 841s 3 7587 10267 841s 4 10268 14658 841s startRow endRow 841s 1 10 7574 841s startRow endRow 841s 1 1 7586 841s Total CN segmentation table (expanded): 841s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 841s 1 1 554484 120992603 7586 1.3853 2108 2108 841s (TCN,DH) segmentation for one total CN segment: 841s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 841s 1 1 1 1 554484 120992603 7586 1.3853 2108 841s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 841s 1 2108 554484 120992603 2108 0.5116 841s Total CN segment #1 ([ 554484,1.20993e+08]) of 4...done 841s Total CN segment #2 ([ NA, NA]) of 4... 841s No signals to segment. Just a "splitter" segment. Skipping. 841s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 841s NA 2 1 NA NA NA NA NA 0 841s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 841s NA 0 NA NA 0 NA 841s Total CN segment #2 ([ NA, NA]) of 4...done 841s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4... 841s Number of TCN loci in segment: 2681 841s Locus data for TCN segment: 841s 'data.frame': 2681 obs. of 9 variables: 841s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 841s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 841s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 841s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 841s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 841s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 841s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 841s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 841s $ rho : num 0.117 0.258 NA NA NA ... 841s Number of loci: 2681 841s Number of SNPs: 777 (28.98%) 841s Number of heterozygous SNPs: 777 (100.00%) 841s Chromosome: 1 841s Segmenting DH signals... 841s Segmenting by CBS... 841s Chromosome: 1 841s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 841s Segmenting by CBS...done 841s List of 4 841s $ data :'data.frame': 2681 obs. of 4 variables: 841s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 841s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 841s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 841s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 841s $ output :'data.frame': 1 obs. of 6 variables: 841s ..$ sampleName: chr NA 841s ..$ chromosome: int 1 841s ..$ start : num 1.42e+08 841s ..$ end : num 1.85e+08 841s ..$ nbrOfLoci : int 777 841s ..$ mean : num 0.0973 841s $ segRows:'data.frame': 1 obs. of 2 variables: 841s ..$ startRow: int 1 841s ..$ endRow : int 2677 841s $ params :List of 5 841s ..$ alpha : num 0.001 841s ..$ undo : num 0 841s ..$ joinSegments : logi TRUE 841s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 841s .. ..$ chromosome: int 1 841s .. ..$ start : num 1.42e+08 841s .. ..$ end : num 1.85e+08 841s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 841s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 841s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.064 0 0.063 0 0 841s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 841s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 841s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 841s DH segmentation (locally-indexed) rows: 841s startRow endRow 841s 1 1 2677 841s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 841s DH segmentation rows: 841s startRow endRow 841s 1 7587 10263 841s Segmenting DH signals...done 841s DH segmentation table: 841s dhStart dhEnd dhNbrOfLoci dhMean 841s 1 141510003 185449813 777 0.0973 841s startRow endRow 841s 1 7587 10263 841s Rows: 841s [1] 3 841s TCN segmentation rows: 841s startRow endRow 841s 3 7587 10267 841s TCN and DH segmentation rows: 841s startRow endRow 841s 3 7587 10267 841s startRow endRow 841s 1 7587 10263 841s startRow endRow 841s 1 1 7586 841s NA NA NA 841s TCN segmentation (expanded) rows: 841s startRow endRow 841s 1 1 7586 841s NA NA NA 841s 3 7587 10267 841s TCN and DH segmentation rows: 841s startRow endRow 841s 1 1 7586 841s 2 NA NA 841s 3 7587 10267 841s 4 10268 14658 841s startRow endRow 841s 1 10 7574 841s 2 NA NA 841s 3 7587 10263 841s startRow endRow 841s 1 1 7586 841s 2 NA NA 841s 3 7587 10267 841s Total CN segmentation table (expanded): 841s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 841s 3 1 141510003 185449813 2681 2.0689 777 777 841s (TCN,DH) segmentation for one total CN segment: 841s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 841s 3 3 1 1 141510003 185449813 2681 2.0689 777 841s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 841s 3 777 141510003 185449813 777 0.0973 841s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4...done 841s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4... 841s Number of TCN loci in segment: 4391 841s Locus data for TCN segment: 841s 'data.frame': 4391 obs. of 9 variables: 841s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 841s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 841s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 841s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 841s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 841s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 841s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 841s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 841s $ rho : num NA 0.2186 NA 0.0503 NA ... 841s Number of loci: 4391 841s Number of SNPs: 1311 (29.86%) 841s Number of heterozygous SNPs: 1311 (100.00%) 841s Chromosome: 1 841s Segmenting DH signals... 841s Segmenting by CBS... 841s Chromosome: 1 841s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 841s Segmenting by CBS...done 841s List of 4 841s $ data :'data.frame': 4391 obs. of 4 variables: 841s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 841s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 841s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 841s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 841s $ output :'data.frame': 1 obs. of 6 variables: 841s ..$ sampleName: chr NA 841s ..$ chromosome: int 1 841s ..$ start : num 1.85e+08 841s ..$ end : num 2.47e+08 841s ..$ nbrOfLoci : int 1311 841s ..$ mean : num 0.23 841s $ segRows:'data.frame': 1 obs. of 2 variables: 841s ..$ startRow: int 2 841s ..$ endRow : int 4388 841s $ params :List of 5 841s ..$ alpha : num 0.001 841s ..$ undo : num 0 841s ..$ joinSegments : logi TRUE 841s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 841s .. ..$ chromosome: int 1 841s .. ..$ start : num 1.85e+08 841s .. ..$ end : num 2.47e+08 841s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 841s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 841s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.194 0.003 0.197 0 0 841s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 841s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 841s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 841s DH segmentation (locally-indexed) rows: 841s startRow endRow 841s 1 2 4388 841s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 841s DH segmentation rows: 841s startRow endRow 841s 1 10269 14655 841s Segmenting DH signals...done 841s DH segmentation table: 841s dhStart dhEnd dhNbrOfLoci dhMean 841s 1 185449813 247137334 1311 0.2295 841s startRow endRow 841s 1 10269 14655 841s Rows: 841s [1] 4 841s TCN segmentation rows: 841s startRow endRow 841s 4 10268 14658 841s TCN and DH segmentation rows: 841s startRow endRow 841s 4 10268 14658 841s startRow endRow 841s 1 10269 14655 841s startRow endRow 841s 1 1 7586 841s 2 NA NA 841s 3 7587 10267 841s TCN segmentation (expanded) rows: 841s startRow endRow 841s 1 1 7586 841s 2 NA NA 841s 3 7587 10267 841s 4 10268 14658 841s TCN and DH segmentation rows: 841s startRow endRow 841s 1 1 7586 841s 2 NA NA 841s 3 7587 10267 841s 4 10268 14658 841s startRow endRow 841s 1 10 7574 841s 2 NA NA 841s 3 7587 10263 841s 4 10269 14655 841s startRow endRow 841s 1 1 7586 841s 2 NA NA 841s 3 7587 10267 841s 4 10268 14658 841s Total CN segmentation table (expanded): 841s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 841s 4 1 185449813 247137334 4391 2.6341 1311 1311 841s (TCN,DH) segmentation for one total CN segment: 841s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 841s 4 4 1 1 185449813 247137334 4391 2.6341 1311 841s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 841s 4 1311 185449813 247137334 1311 0.2295 841s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4...done 841s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 841s 1 1 1 1 554484 120992603 7586 1.3853 2108 841s 2 NA 2 1 NA NA NA NA 0 841s 3 1 3 1 141510003 185449813 2681 2.0689 777 841s 4 1 4 1 185449813 247137334 4391 2.6341 1311 841s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 841s 1 2108 554484 120992603 2108 0.5116 841s 2 0 NA NA 0 NA 841s 3 777 141510003 185449813 777 0.0973 841s 4 1311 185449813 247137334 1311 0.2295 841s Calculating (C1,C2) per segment... 841s Calculating (C1,C2) per segment...done 841s Number of segments: 4 841s Segmenting paired tumor-normal signals using Paired PSCBS...done 841s Post-segmenting TCNs... 841s Number of segments: 3 841s Number of chromosomes: 1 841s [1] 1 841s Chromosome 1 ('chr01') of 1... 841s Rows: 841s [1] 1 2 3 841s Number of segments: 3 841s TCN segment #1 ('1') of 3... 841s Nothing todo. Only one DH segmentation. Skipping. 841s TCN segment #1 ('1') of 3...done 841s TCN segment #2 ('3') of 3... 841s Nothing todo. Only one DH segmentation. Skipping. 841s TCN segment #2 ('3') of 3...done 841s TCN segment #3 ('4') of 3... 841s Nothing todo. Only one DH segmentation. Skipping. 841s TCN segment #3 ('4') of 3...done 841s Chromosome 1 ('chr01') of 1...done 841s Update (C1,C2) per segment... 841s Update (C1,C2) per segment...done 841s Post-segmenting TCNs...done 841s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 841s 1 1 1 1 554484 120992603 7586 1.3853 2108 841s 2 NA 2 1 NA NA NA NA 0 841s 3 1 3 1 141510003 185449813 2681 2.0689 777 841s 4 1 4 1 185449813 247137334 4391 2.6341 1311 841s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 841s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 841s 2 0 NA NA 0 NA NA NA 841s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 841s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 841s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 841s 1 1 1 1 554484 120992603 7586 1.3853 2108 841s 2 NA 2 1 NA NA NA NA 0 841s 3 1 3 1 141510003 185449813 2681 2.0689 777 841s 4 1 4 1 185449813 247137334 4391 2.6341 1311 841s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 841s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 841s 2 0 NA NA 0 NA NA NA 841s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 841s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 841s > print(fit) 841s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 841s 1 1 1 1 554484 120992603 7586 1.3853 2108 841s 2 NA 2 1 NA NA NA NA 0 841s 3 1 3 1 141510003 185449813 2681 2.0689 777 841s 4 1 4 1 185449813 247137334 4391 2.6341 1311 841s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 841s 1 2108 2108 0.5116 0.3382903 1.047010 841s 2 0 0 NA NA NA 841s 3 777 777 0.0973 0.9337980 1.135102 841s 4 1311 1311 0.2295 1.0147870 1.619313 841s > 841s > # Plot results 841s > dev.set(2L) 841s null device 841s 1 841s > plotTracks(fit) 841s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 841s > 841s > # Sanity check 841s > stopifnot(nbrOfSegments(fit) == nSegs) 841s > 841s > fit1 <- fit 841s > 841s > 841s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 841s > # (b) Segment also the centromere (which will become NAs) 841s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 841s > knownSegments <- data.frame( 841s + chromosome = c( 1, 1, 1), 841s + start = c( -Inf, 120992604, 141510003), 841s + end = c(120992603, 141510002, +Inf) 841s + ) 841s > 841s > 841s > # Paired PSCBS segmentation 841s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 841s + seed=0xBEEF, verbose=-10) 841s Segmenting paired tumor-normal signals using Paired PSCBS... 841s Calling genotypes from normal allele B fractions... 841s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 841s Called genotypes: 841s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 841s - attr(*, "modelFit")=List of 1 841s ..$ :List of 7 841s .. ..$ flavor : chr "density" 841s .. ..$ cn : int 2 841s .. ..$ nbrOfGenotypeGroups: int 3 841s .. ..$ tau : num [1:2] 0.315 0.677 841s .. ..$ n : int 14640 841s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 841s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 841s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 841s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 841s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 841s .. .. ..$ type : chr [1:2] "valley" "valley" 841s .. .. ..$ x : num [1:2] 0.315 0.677 841s .. .. ..$ density: num [1:2] 0.522 0.552 841s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 841s muN 841s 0 0.5 1 841s 5221 4198 5251 841s Calling genotypes from normal allele B fractions...done 841s Normalizing betaT using betaN (TumorBoost)... 841s Normalized BAFs: 841s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 841s - attr(*, "modelFit")=List of 5 841s ..$ method : chr "normalizeTumorBoost" 841s ..$ flavor : chr "v4" 841s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 841s .. ..- attr(*, "modelFit")=List of 1 841s .. .. ..$ :List of 7 841s .. .. .. ..$ flavor : chr "density" 841s .. .. .. ..$ cn : int 2 841s .. .. .. ..$ nbrOfGenotypeGroups: int 3 841s .. .. .. ..$ tau : num [1:2] 0.315 0.677 841s .. .. .. ..$ n : int 14640 841s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 841s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 841s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 841s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 841s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 841s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 841s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 841s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 841s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 841s ..$ preserveScale: logi FALSE 841s ..$ scaleFactor : num NA 841s Normalizing betaT using betaN (TumorBoost)...done 841s Setup up data... 841s 'data.frame': 14670 obs. of 7 variables: 841s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 841s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 841s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 841s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 841s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 841s ..- attr(*, "modelFit")=List of 5 841s .. ..$ method : chr "normalizeTumorBoost" 841s .. ..$ flavor : chr "v4" 841s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 841s .. .. ..- attr(*, "modelFit")=List of 1 841s .. .. .. ..$ :List of 7 841s .. .. .. .. ..$ flavor : chr "density" 842s .. .. .. .. ..$ cn : int 2 842s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 842s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 842s .. .. .. .. ..$ n : int 14640 842s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 842s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 842s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 842s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 842s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 842s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 842s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 842s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 842s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 842s .. ..$ preserveScale: logi FALSE 842s .. ..$ scaleFactor : num NA 842s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 842s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 842s ..- attr(*, "modelFit")=List of 1 842s .. ..$ :List of 7 842s .. .. ..$ flavor : chr "density" 842s .. .. ..$ cn : int 2 842s .. .. ..$ nbrOfGenotypeGroups: int 3 842s .. .. ..$ tau : num [1:2] 0.315 0.677 842s .. .. ..$ n : int 14640 842s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 842s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 842s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 842s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 842s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 842s .. .. .. ..$ type : chr [1:2] "valley" "valley" 842s .. .. .. ..$ x : num [1:2] 0.315 0.677 842s .. .. .. ..$ density: num [1:2] 0.522 0.552 842s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 842s Setup up data...done 842s Dropping loci for which TCNs are missing... 842s Number of loci dropped: 12 842s Dropping loci for which TCNs are missing...done 842s Ordering data along genome... 842s 'data.frame': 14658 obs. of 7 variables: 842s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 842s $ x : num 554484 730720 782343 878522 916294 ... 842s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 842s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 842s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 842s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 842s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 842s Ordering data along genome...done 842s Keeping only current chromosome for 'knownSegments'... 842s Chromosome: 1 842s Known segments for this chromosome: 842s chromosome start end 842s 1 1 -Inf 120992603 842s 2 1 120992604 141510002 842s 3 1 141510003 Inf 842s Keeping only current chromosome for 'knownSegments'...done 842s alphaTCN: 0.009 842s alphaDH: 0.001 842s Number of loci: 14658 842s Calculating DHs... 842s Number of SNPs: 14658 842s Number of heterozygous SNPs: 4196 (28.63%) 842s Normalized DHs: 842s num [1:14658] NA NA NA NA NA ... 842s Calculating DHs...done 842s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 842s Produced 2 seeds from this stream for future usage 842s Identification of change points by total copy numbers... 842s Segmenting by CBS... 842s Chromosome: 1 842s Segmenting multiple segments on current chromosome... 842s Number of segments: 3 842s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 842s Produced 3 seeds from this stream for future usage 842s Segmenting by CBS... 842s Chromosome: 1 842s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 842s Segmenting by CBS...done 842s Segmenting by CBS... 842s Chromosome: 1 842s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 842s Segmenting by CBS...done 842s Segmenting multiple segments on current chromosome...done 842s Segmenting by CBS...done 842s List of 4 842s $ data :'data.frame': 14658 obs. of 4 variables: 842s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 842s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 842s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 842s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 842s $ output :'data.frame': 4 obs. of 6 variables: 842s ..$ sampleName: chr [1:4] NA NA NA NA 842s ..$ chromosome: num [1:4] 1 1 1 1 842s ..$ start : num [1:4] 5.54e+05 1.21e+08 1.42e+08 1.85e+08 842s ..$ end : num [1:4] 1.21e+08 1.42e+08 1.85e+08 2.47e+08 842s ..$ nbrOfLoci : int [1:4] 7586 0 2681 4391 842s ..$ mean : num [1:4] 1.39 NA 2.07 2.63 842s $ segRows:'data.frame': 4 obs. of 2 variables: 842s ..$ startRow: int [1:4] 1 NA 7587 10268 842s ..$ endRow : int [1:4] 7586 NA 10267 14658 842s $ params :List of 5 842s ..$ alpha : num 0.009 842s ..$ undo : num 0 842s ..$ joinSegments : logi TRUE 842s ..$ knownSegments:'data.frame': 4 obs. of 3 variables: 842s .. ..$ chromosome: num [1:4] 1 1 2 1 842s .. ..$ start : num [1:4] -Inf -Inf -Inf 1.42e+08 842s .. ..$ end : num [1:4] 1.21e+08 Inf Inf Inf 842s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 842s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 842s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.704 0 0.705 0 0 842s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 842s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 842s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s Identification of change points by total copy numbers...done 842s Restructure TCN segmentation results... 842s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 842s 1 1 554484 120992603 7586 1.3853 842s 2 1 120992604 141510002 0 NA 842s 3 1 141510003 185449813 2681 2.0689 842s 4 1 185449813 247137334 4391 2.6341 842s Number of TCN segments: 4 842s Restructure TCN segmentation results...done 842s Total CN segment #1 ([ 554484,1.20993e+08]) of 4... 842s Number of TCN loci in segment: 7586 842s Locus data for TCN segment: 842s 'data.frame': 7586 obs. of 9 variables: 842s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 842s $ x : num 554484 730720 782343 878522 916294 ... 842s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 842s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 842s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 842s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 842s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 842s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 842s $ rho : num NA NA NA NA NA ... 842s Number of loci: 7586 842s Number of SNPs: 2108 (27.79%) 842s Number of heterozygous SNPs: 2108 (100.00%) 842s Chromosome: 1 842s Segmenting DH signals... 842s Segmenting by CBS... 842s Chromosome: 1 842s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 842s Segmenting by CBS...done 842s List of 4 842s $ data :'data.frame': 7586 obs. of 4 variables: 842s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 842s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 842s ..$ y : num [1:7586] NA NA NA NA NA ... 842s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 842s $ output :'data.frame': 1 obs. of 6 variables: 842s ..$ sampleName: chr NA 842s ..$ chromosome: int 1 842s ..$ start : num 554484 842s ..$ end : num 1.21e+08 842s ..$ nbrOfLoci : int 2108 842s ..$ mean : num 0.512 842s $ segRows:'data.frame': 1 obs. of 2 variables: 842s ..$ startRow: int 10 842s ..$ endRow : int 7574 842s $ params :List of 5 842s ..$ alpha : num 0.001 842s ..$ undo : num 0 842s ..$ joinSegments : logi TRUE 842s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 842s .. ..$ chromosome: int 1 842s .. ..$ start : num 554484 842s .. ..$ end : num 1.21e+08 842s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 842s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.117 0 0.118 0 0 842s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 842s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 842s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s DH segmentation (locally-indexed) rows: 842s startRow endRow 842s 1 10 7574 842s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 842s DH segmentation rows: 842s startRow endRow 842s 1 10 7574 842s Segmenting DH signals...done 842s DH segmentation table: 842s dhStart dhEnd dhNbrOfLoci dhMean 842s 1 554484 120992603 2108 0.5116 842s startRow endRow 842s 1 10 7574 842s Rows: 842s [1] 1 842s TCN segmentation rows: 842s startRow endRow 842s 1 1 7586 842s TCN and DH segmentation rows: 842s startRow endRow 842s 1 1 7586 842s startRow endRow 842s 1 10 7574 842s NULL 842s TCN segmentation (expanded) rows: 842s startRow endRow 842s 1 1 7586 842s TCN and DH segmentation rows: 842s startRow endRow 842s 1 1 7586 842s 2 NA NA 842s 3 7587 10267 842s 4 10268 14658 842s startRow endRow 842s 1 10 7574 842s startRow endRow 842s 1 1 7586 842s Total CN segmentation table (expanded): 842s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 842s 1 1 554484 120992603 7586 1.3853 2108 2108 842s (TCN,DH) segmentation for one total CN segment: 842s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 1 1 1 1 554484 120992603 7586 1.3853 2108 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 842s 1 2108 554484 120992603 2108 0.5116 842s Total CN segment #1 ([ 554484,1.20993e+08]) of 4...done 842s Total CN segment #2 ([1.20993e+08,1.4151e+08]) of 4... 842s Number of TCN loci in segment: 0 842s Locus data for TCN segment: 842s 'data.frame': 0 obs. of 9 variables: 842s $ chromosome: int 842s $ x : num 842s $ CT : num 842s $ betaT : num 842s $ betaTN : num 842s $ betaN : num 842s $ muN : num 842s $ index : int 842s $ rho : num 842s Number of loci: 0 842s Number of SNPs: 0 (NaN%) 842s Number of heterozygous SNPs: 0 (NaN%) 842s Chromosome: 1 842s Segmenting DH signals... 842s Segmenting by CBS... 842s Chromosome: NA 842s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 842s Segmenting by CBS...done 842s List of 4 842s $ data :'data.frame': 0 obs. of 4 variables: 842s ..$ chromosome: int(0) 842s ..$ x : num(0) 842s ..$ y : num(0) 842s ..$ index : int(0) 842s $ output :'data.frame': 0 obs. of 6 variables: 842s ..$ sampleName: chr(0) 842s ..$ chromosome: num(0) 842s ..$ start : num(0) 842s ..$ end : num(0) 842s ..$ nbrOfLoci : int(0) 842s ..$ mean : num(0) 842s $ segRows:'data.frame': 0 obs. of 2 variables: 842s ..$ startRow: int(0) 842s ..$ endRow : int(0) 842s $ params :List of 5 842s ..$ alpha : num 0.001 842s ..$ undo : num 0 842s ..$ joinSegments : logi TRUE 842s ..$ knownSegments:'data.frame': 0 obs. of 3 variables: 842s .. ..$ chromosome: int(0) 842s .. ..$ start : num(0) 842s .. ..$ end : num(0) 842s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 842s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.009 0 0.008 0 0 842s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 842s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 842s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s DH segmentation (locally-indexed) rows: 842s [1] startRow endRow 842s <0 rows> (or 0-length row.names) 842s int(0) 842s DH segmentation rows: 842s [1] startRow endRow 842s <0 rows> (or 0-length row.names) 842s Segmenting DH signals...done 842s DH segmentation table: 842s dhStart dhEnd dhNbrOfLoci dhMean 842s NA NA NA NA NA 842s startRow endRow 842s NA NA NA 842s Rows: 842s [1] 2 842s TCN segmentation rows: 842s startRow endRow 842s 2 NA NA 842s TCN and DH segmentation rows: 842s startRow endRow 842s 2 NA NA 842s startRow endRow 842s NA NA NA 842s startRow endRow 842s 1 1 7586 842s TCN segmentation (expanded) rows: 842s startRow endRow 842s 1 1 7586 842s 2 NA NA 842s TCN and DH segmentation rows: 842s startRow endRow 842s 1 1 7586 842s 2 NA NA 842s 3 7587 10267 842s 4 10268 14658 842s startRow endRow 842s 1 10 7574 842s 2 NA NA 842s startRow endRow 842s 1 1 7586 842s 2 NA NA 842s Total CN segmentation table (expanded): 842s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 842s 2 1 120992604 141510002 0 NA 0 0 842s (TCN,DH) segmentation for one total CN segment: 842s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 2 2 1 1 120992604 141510002 0 NA 0 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 842s 2 0 NA NA NA NA 842s Total CN segment #2 ([1.20993e+08,1.4151e+08]) of 4...done 842s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4... 842s Number of TCN loci in segment: 2681 842s Locus data for TCN segment: 842s 'data.frame': 2681 obs. of 9 variables: 842s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 842s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 842s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 842s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 842s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 842s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 842s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 842s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 842s $ rho : num 0.117 0.258 NA NA NA ... 842s Number of loci: 2681 842s Number of SNPs: 777 (28.98%) 842s Number of heterozygous SNPs: 777 (100.00%) 842s Chromosome: 1 842s Segmenting DH signals... 842s Segmenting by CBS... 842s Chromosome: 1 842s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 842s Segmenting by CBS...done 842s List of 4 842s $ data :'data.frame': 2681 obs. of 4 variables: 842s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 842s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 842s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 842s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 842s $ output :'data.frame': 1 obs. of 6 variables: 842s ..$ sampleName: chr NA 842s ..$ chromosome: int 1 842s ..$ start : num 1.42e+08 842s ..$ end : num 1.85e+08 842s ..$ nbrOfLoci : int 777 842s ..$ mean : num 0.0973 842s $ segRows:'data.frame': 1 obs. of 2 variables: 842s ..$ startRow: int 1 842s ..$ endRow : int 2677 842s $ params :List of 5 842s ..$ alpha : num 0.001 842s ..$ undo : num 0 842s ..$ joinSegments : logi TRUE 842s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 842s .. ..$ chromosome: int 1 842s .. ..$ start : num 1.42e+08 842s .. ..$ end : num 1.85e+08 842s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 842s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.064 0 0.063 0 0 842s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 842s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 842s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s DH segmentation (locally-indexed) rows: 842s startRow endRow 842s 1 1 2677 842s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 842s DH segmentation rows: 842s startRow endRow 842s 1 7587 10263 842s Segmenting DH signals...done 842s DH segmentation table: 842s dhStart dhEnd dhNbrOfLoci dhMean 842s 1 141510003 185449813 777 0.0973 842s startRow endRow 842s 1 7587 10263 842s Rows: 842s [1] 3 842s TCN segmentation rows: 842s startRow endRow 842s 3 7587 10267 842s TCN and DH segmentation rows: 842s startRow endRow 842s 3 7587 10267 842s startRow endRow 842s 1 7587 10263 842s startRow endRow 842s 1 1 7586 842s 2 NA NA 842s TCN segmentation (expanded) rows: 842s startRow endRow 842s 1 1 7586 842s 2 NA NA 842s 3 7587 10267 842s TCN and DH segmentation rows: 842s startRow endRow 842s 1 1 7586 842s 2 NA NA 842s 3 7587 10267 842s 4 10268 14658 842s startRow endRow 842s 1 10 7574 842s 2 NA NA 842s 3 7587 10263 842s startRow endRow 842s 1 1 7586 842s 2 NA NA 842s 3 7587 10267 842s Total CN segmentation table (expanded): 842s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 842s 3 1 141510003 185449813 2681 2.0689 777 777 842s (TCN,DH) segmentation for one total CN segment: 842s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 3 3 1 1 141510003 185449813 2681 2.0689 777 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 842s 3 777 141510003 185449813 777 0.0973 842s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4...done 842s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4... 842s Number of TCN loci in segment: 4391 842s Locus data for TCN segment: 842s 'data.frame': 4391 obs. of 9 variables: 842s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 842s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 842s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 842s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 842s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 842s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 842s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 842s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 842s $ rho : num NA 0.2186 NA 0.0503 NA ... 842s Number of loci: 4391 842s Number of SNPs: 1311 (29.86%) 842s Number of heterozygous SNPs: 1311 (100.00%) 842s Chromosome: 1 842s Segmenting DH signals... 842s Segmenting by CBS... 842s Chromosome: 1 842s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 842s Segmenting by CBS...done 842s List of 4 842s $ data :'data.frame': 4391 obs. of 4 variables: 842s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 842s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 842s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 842s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 842s $ output :'data.frame': 1 obs. of 6 variables: 842s ..$ sampleName: chr NA 842s ..$ chromosome: int 1 842s ..$ start : num 1.85e+08 842s ..$ end : num 2.47e+08 842s ..$ nbrOfLoci : int 1311 842s ..$ mean : num 0.23 842s $ segRows:'data.frame': 1 obs. of 2 variables: 842s ..$ startRow: int 2 842s ..$ endRow : int 4388 842s $ params :List of 5 842s ..$ alpha : num 0.001 842s ..$ undo : num 0 842s ..$ joinSegments : logi TRUE 842s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 842s .. ..$ chromosome: int 1 842s .. ..$ start : num 1.85e+08 842s .. ..$ end : num 2.47e+08 842s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 842s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.105 0 0.107 0 0 842s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 842s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 842s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s DH segmentation (locally-indexed) rows: 842s startRow endRow 842s 1 2 4388 842s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 842s DH segmentation rows: 842s startRow endRow 842s 1 10269 14655 842s Segmenting DH signals...done 842s DH segmentation table: 842s dhStart dhEnd dhNbrOfLoci dhMean 842s 1 185449813 247137334 1311 0.2295 842s startRow endRow 842s 1 10269 14655 842s Rows: 842s [1] 4 842s TCN segmentation rows: 842s startRow endRow 842s 4 10268 14658 842s TCN and DH segmentation rows: 842s startRow endRow 842s 4 10268 14658 842s startRow endRow 842s 1 10269 14655 842s startRow endRow 842s 1 1 7586 842s 2 NA NA 842s 3 7587 10267 842s TCN segmentation (expanded) rows: 842s startRow endRow 842s 1 1 7586 842s 2 NA NA 842s 3 7587 10267 842s 4 10268 14658 842s TCN and DH segmentation rows: 842s startRow endRow 842s 1 1 7586 842s 2 NA NA 842s 3 7587 10267 842s 4 10268 14658 842s startRow endRow 842s 1 10 7574 842s 2 NA NA 842s 3 7587 10263 842s 4 10269 14655 842s startRow endRow 842s 1 1 7586 842s 2 NA NA 842s 3 7587 10267 842s 4 10268 14658 842s Total CN segmentation table (expanded): 842s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 842s 4 1 185449813 247137334 4391 2.6341 1311 1311 842s (TCN,DH) segmentation for one total CN segment: 842s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 4 4 1 1 185449813 247137334 4391 2.6341 1311 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 842s 4 1311 185449813 247137334 1311 0.2295 842s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4...done 842s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 1 1 1 1 554484 120992603 7586 1.3853 2108 842s 2 1 2 1 120992604 141510002 0 NA 0 842s 3 1 3 1 141510003 185449813 2681 2.0689 777 842s 4 1 4 1 185449813 247137334 4391 2.6341 1311 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 842s 1 2108 554484 120992603 2108 0.5116 842s 2 0 NA NA NA NA 842s 3 777 141510003 185449813 777 0.0973 842s 4 1311 185449813 247137334 1311 0.2295 842s Calculating (C1,C2) per segment... 842s Calculating (C1,C2) per segment...done 842s Number of segments: 4 842s Segmenting paired tumor-normal signals using Paired PSCBS...done 842s Post-segmenting TCNs... 842s Number of segments: 4 842s Number of chromosomes: 1 842s [1] 1 842s Chromosome 1 ('chr01') of 1... 842s Rows: 842s [1] 1 2 3 4 842s Number of segments: 4 842s TCN segment #1 ('1') of 4... 842s Nothing todo. Only one DH segmentation. Skipping. 842s TCN segment #1 ('1') of 4...done 842s TCN segment #2 ('2') of 4... 842s Nothing todo. Only one DH segmentation. Skipping. 842s TCN segment #2 ('2') of 4...done 842s TCN segment #3 ('3') of 4... 842s Nothing todo. Only one DH segmentation. Skipping. 842s TCN segment #3 ('3') of 4...done 842s TCN segment #4 ('4') of 4... 842s Nothing todo. Only one DH segmentation. Skipping. 842s TCN segment #4 ('4') of 4...done 842s Chromosome 1 ('chr01') of 1...done 842s Update (C1,C2) per segment... 842s Update (C1,C2) per segment...done 842s Post-segmenting TCNs...done 842s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 1 1 1 1 554484 120992603 7586 1.3853 2108 842s 2 1 2 1 120992604 141510002 0 NA 0 842s 3 1 3 1 141510003 185449813 2681 2.0689 777 842s 4 1 4 1 185449813 247137334 4391 2.6341 1311 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 842s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 842s 2 0 NA NA NA NA NA NA 842s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 842s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 842s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 1 1 1 1 554484 120992603 7586 1.3853 2108 842s 2 1 2 1 120992604 141510002 0 NA 0 842s 3 1 3 1 141510003 185449813 2681 2.0689 777 842s 4 1 4 1 185449813 247137334 4391 2.6341 1311 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 842s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 842s 2 0 NA NA NA NA NA NA 842s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 842s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 842s > print(fit) 842s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 1 1 1 1 554484 120992603 7586 1.3853 2108 842s 2 1 2 1 120992604 141510002 0 NA 0 842s 3 1 3 1 141510003 185449813 2681 2.0689 777 842s 4 1 4 1 185449813 247137334 4391 2.6341 1311 842s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 842s 1 2108 2108 0.5116 0.3382903 1.047010 842s 2 0 NA NA NA NA 842s 3 777 777 0.0973 0.9337980 1.135102 842s 4 1311 1311 0.2295 1.0147870 1.619313 842s > 842s > # Plot results 842s > dev.set(3L) 842s pdf 842s 2 842s > plotTracks(fit) 842s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 842s > 842s > # Sanity check [TO FIX: See above] 842s > stopifnot(nbrOfSegments(fit) == nSegs) 842s > 842s > fit2 <- fit 842s > 842s > 842s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 842s > # (c) Do not segment the centromere (without a separator) 842s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 842s > knownSegments <- data.frame( 842s + chromosome = c( 1, 1), 842s + start = c( -Inf, 141510003), 842s + end = c(120992603, +Inf) 842s + ) 842s > 842s > # Paired PSCBS segmentation 842s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 842s + seed=0xBEEF, verbose=-10) 842s Segmenting paired tumor-normal signals using Paired PSCBS... 842s Calling genotypes from normal allele B fractions... 842s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 842s Called genotypes: 842s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 842s - attr(*, "modelFit")=List of 1 842s ..$ :List of 7 842s .. ..$ flavor : chr "density" 842s .. ..$ cn : int 2 842s .. ..$ nbrOfGenotypeGroups: int 3 842s .. ..$ tau : num [1:2] 0.315 0.677 842s .. ..$ n : int 14640 842s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 842s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 842s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 842s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 842s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 842s .. .. ..$ type : chr [1:2] "valley" "valley" 842s .. .. ..$ x : num [1:2] 0.315 0.677 842s .. .. ..$ density: num [1:2] 0.522 0.552 842s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 842s muN 842s 0 0.5 1 842s 5221 4198 5251 842s Calling genotypes from normal allele B fractions...done 842s Normalizing betaT using betaN (TumorBoost)... 842s Normalized BAFs: 842s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 842s - attr(*, "modelFit")=List of 5 842s ..$ method : chr "normalizeTumorBoost" 842s ..$ flavor : chr "v4" 842s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 842s .. ..- attr(*, "modelFit")=List of 1 842s .. .. ..$ :List of 7 842s .. .. .. ..$ flavor : chr "density" 842s .. .. .. ..$ cn : int 2 842s .. .. .. ..$ nbrOfGenotypeGroups: int 3 842s .. .. .. ..$ tau : num [1:2] 0.315 0.677 842s .. .. .. ..$ n : int 14640 842s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 842s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 842s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 842s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 842s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 842s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 842s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 842s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 842s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 842s ..$ preserveScale: logi FALSE 842s ..$ scaleFactor : num NA 842s Normalizing betaT using betaN (TumorBoost)...done 842s Setup up data... 842s 'data.frame': 14670 obs. of 7 variables: 842s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 842s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 842s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 842s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 842s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 842s ..- attr(*, "modelFit")=List of 5 842s .. ..$ method : chr "normalizeTumorBoost" 842s .. ..$ flavor : chr "v4" 842s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 842s .. .. ..- attr(*, "modelFit")=List of 1 842s .. .. .. ..$ :List of 7 842s .. .. .. .. ..$ flavor : chr "density" 842s .. .. .. .. ..$ cn : int 2 842s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 842s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 842s .. .. .. .. ..$ n : int 14640 842s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 842s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 842s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 842s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 842s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 842s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 842s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 842s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 842s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 842s .. ..$ preserveScale: logi FALSE 842s .. ..$ scaleFactor : num NA 842s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 842s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 842s ..- attr(*, "modelFit")=List of 1 842s .. ..$ :List of 7 842s .. .. ..$ flavor : chr "density" 842s .. .. ..$ cn : int 2 842s .. .. ..$ nbrOfGenotypeGroups: int 3 842s .. .. ..$ tau : num [1:2] 0.315 0.677 842s .. .. ..$ n : int 14640 842s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 842s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 842s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 842s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 842s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 842s .. .. .. ..$ type : chr [1:2] "valley" "valley" 842s .. .. .. ..$ x : num [1:2] 0.315 0.677 842s .. .. .. ..$ density: num [1:2] 0.522 0.552 842s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 842s Setup up data...done 842s Dropping loci for which TCNs are missing... 842s Number of loci dropped: 12 842s Dropping loci for which TCNs are missing...done 842s Ordering data along genome... 842s 'data.frame': 14658 obs. of 7 variables: 842s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 842s $ x : num 554484 730720 782343 878522 916294 ... 842s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 842s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 842s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 842s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 842s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 842s Ordering data along genome...done 842s Keeping only current chromosome for 'knownSegments'... 842s Chromosome: 1 842s Known segments for this chromosome: 842s chromosome start end 842s 1 1 -Inf 120992603 842s 2 1 141510003 Inf 842s Keeping only current chromosome for 'knownSegments'...done 842s alphaTCN: 0.009 842s alphaDH: 0.001 842s Number of loci: 14658 842s Calculating DHs... 842s Number of SNPs: 14658 842s Number of heterozygous SNPs: 4196 (28.63%) 842s Normalized DHs: 842s num [1:14658] NA NA NA NA NA ... 842s Calculating DHs...done 842s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 842s Produced 2 seeds from this stream for future usage 842s Identification of change points by total copy numbers... 842s Segmenting by CBS... 842s Chromosome: 1 842s Segmenting multiple segments on current chromosome... 842s Number of segments: 2 842s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 842s Produced 2 seeds from this stream for future usage 842s Segmenting by CBS... 842s Chromosome: 1 842s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 842s Segmenting by CBS...done 842s Segmenting by CBS... 842s Chromosome: 1 842s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 842s Segmenting by CBS...done 842s Segmenting multiple segments on current chromosome...done 842s Segmenting by CBS...done 842s List of 4 842s $ data :'data.frame': 14658 obs. of 4 variables: 842s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 842s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 842s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 842s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 842s $ output :'data.frame': 3 obs. of 6 variables: 842s ..$ sampleName: chr [1:3] NA NA NA 842s ..$ chromosome: int [1:3] 1 1 1 842s ..$ start : num [1:3] 5.54e+05 1.42e+08 1.85e+08 842s ..$ end : num [1:3] 1.21e+08 1.85e+08 2.47e+08 842s ..$ nbrOfLoci : int [1:3] 7586 2681 4391 842s ..$ mean : num [1:3] 1.39 2.07 2.63 842s $ segRows:'data.frame': 3 obs. of 2 variables: 842s ..$ startRow: int [1:3] 1 7587 10268 842s ..$ endRow : int [1:3] 7586 10267 14658 842s $ params :List of 5 842s ..$ alpha : num 0.009 842s ..$ undo : num 0 842s ..$ joinSegments : logi TRUE 842s ..$ knownSegments:'data.frame': 2 obs. of 3 variables: 842s .. ..$ chromosome: num [1:2] 1 1 842s .. ..$ start : num [1:2] -Inf 1.42e+08 842s .. ..$ end : num [1:2] 1.21e+08 Inf 842s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 842s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 842s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.563 0 0.565 0 0 842s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 842s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 842s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s Identification of change points by total copy numbers...done 842s Restructure TCN segmentation results... 842s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 842s 1 1 554484 120992603 7586 1.3853 842s 2 1 141510003 185449813 2681 2.0689 842s 3 1 185449813 247137334 4391 2.6341 842s Number of TCN segments: 3 842s Restructure TCN segmentation results...done 842s Total CN segment #1 ([ 554484,1.20993e+08]) of 3... 842s Number of TCN loci in segment: 7586 842s Locus data for TCN segment: 842s 'data.frame': 7586 obs. of 9 variables: 842s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 842s $ x : num 554484 730720 782343 878522 916294 ... 842s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 842s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 842s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 842s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 842s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 842s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 842s $ rho : num NA NA NA NA NA ... 842s Number of loci: 7586 842s Number of SNPs: 2108 (27.79%) 842s Number of heterozygous SNPs: 2108 (100.00%) 842s Chromosome: 1 842s Segmenting DH signals... 842s Segmenting by CBS... 842s Chromosome: 1 842s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 842s Segmenting by CBS...done 842s List of 4 842s $ data :'data.frame': 7586 obs. of 4 variables: 842s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 842s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 842s ..$ y : num [1:7586] NA NA NA NA NA ... 842s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 842s $ output :'data.frame': 1 obs. of 6 variables: 842s ..$ sampleName: chr NA 842s ..$ chromosome: int 1 842s ..$ start : num 554484 842s ..$ end : num 1.21e+08 842s ..$ nbrOfLoci : int 2108 842s ..$ mean : num 0.512 842s $ segRows:'data.frame': 1 obs. of 2 variables: 842s ..$ startRow: int 10 842s ..$ endRow : int 7574 842s $ params :List of 5 842s ..$ alpha : num 0.001 842s ..$ undo : num 0 842s ..$ joinSegments : logi TRUE 842s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 842s .. ..$ chromosome: int 1 842s .. ..$ start : num 554484 842s .. ..$ end : num 1.21e+08 842s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 842s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.117 0 0.118 0 0 842s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 842s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 842s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s DH segmentation (locally-indexed) rows: 842s startRow endRow 842s 1 10 7574 842s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 842s DH segmentation rows: 842s startRow endRow 842s 1 10 7574 842s Segmenting DH signals...done 842s DH segmentation table: 842s dhStart dhEnd dhNbrOfLoci dhMean 842s 1 554484 120992603 2108 0.5116 842s startRow endRow 842s 1 10 7574 842s Rows: 842s [1] 1 842s TCN segmentation rows: 842s startRow endRow 842s 1 1 7586 842s TCN and DH segmentation rows: 842s startRow endRow 842s 1 1 7586 842s startRow endRow 842s 1 10 7574 842s NULL 842s TCN segmentation (expanded) rows: 842s startRow endRow 842s 1 1 7586 842s TCN and DH segmentation rows: 842s startRow endRow 842s 1 1 7586 842s 2 7587 10267 842s 3 10268 14658 842s startRow endRow 842s 1 10 7574 842s startRow endRow 842s 1 1 7586 842s Total CN segmentation table (expanded): 842s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 842s 1 1 554484 120992603 7586 1.3853 2108 2108 842s (TCN,DH) segmentation for one total CN segment: 842s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 1 1 1 1 554484 120992603 7586 1.3853 2108 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 842s 1 2108 554484 120992603 2108 0.5116 842s Total CN segment #1 ([ 554484,1.20993e+08]) of 3...done 842s Total CN segment #2 ([1.4151e+08,1.8545e+08]) of 3... 842s Number of TCN loci in segment: 2681 842s Locus data for TCN segment: 842s 'data.frame': 2681 obs. of 9 variables: 842s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 842s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 842s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 842s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 842s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 842s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 842s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 842s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 842s $ rho : num 0.117 0.258 NA NA NA ... 842s Number of loci: 2681 842s Number of SNPs: 777 (28.98%) 842s Number of heterozygous SNPs: 777 (100.00%) 842s Chromosome: 1 842s Segmenting DH signals... 842s Segmenting by CBS... 842s Chromosome: 1 842s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 842s Segmenting by CBS...done 842s List of 4 842s $ data :'data.frame': 2681 obs. of 4 variables: 842s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 842s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 842s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 842s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 842s $ output :'data.frame': 1 obs. of 6 variables: 842s ..$ sampleName: chr NA 842s ..$ chromosome: int 1 842s ..$ start : num 1.42e+08 842s ..$ end : num 1.85e+08 842s ..$ nbrOfLoci : int 777 842s ..$ mean : num 0.0973 842s $ segRows:'data.frame': 1 obs. of 2 variables: 842s ..$ startRow: int 1 842s ..$ endRow : int 2677 842s $ params :List of 5 842s ..$ alpha : num 0.001 842s ..$ undo : num 0 842s ..$ joinSegments : logi TRUE 842s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 842s .. ..$ chromosome: int 1 842s .. ..$ start : num 1.42e+08 842s .. ..$ end : num 1.85e+08 842s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 842s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.045 0 0.044 0 0 842s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 842s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 842s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s DH segmentation (locally-indexed) rows: 842s startRow endRow 842s 1 1 2677 842s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 842s DH segmentation rows: 842s startRow endRow 842s 1 7587 10263 842s Segmenting DH signals...done 842s DH segmentation table: 842s dhStart dhEnd dhNbrOfLoci dhMean 842s 1 141510003 185449813 777 0.0973 842s startRow endRow 842s 1 7587 10263 842s Rows: 842s [1] 2 842s TCN segmentation rows: 842s startRow endRow 842s 2 7587 10267 842s TCN and DH segmentation rows: 842s startRow endRow 842s 2 7587 10267 842s startRow endRow 842s 1 7587 10263 842s startRow endRow 842s 1 1 7586 842s TCN segmentation (expanded) rows: 842s startRow endRow 842s 1 1 7586 842s 2 7587 10267 842s TCN and DH segmentation rows: 842s startRow endRow 842s 1 1 7586 842s 2 7587 10267 842s 3 10268 14658 842s startRow endRow 842s 1 10 7574 842s 2 7587 10263 842s startRow endRow 842s 1 1 7586 842s 2 7587 10267 842s Total CN segmentation table (expanded): 842s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 842s 2 1 141510003 185449813 2681 2.0689 777 777 842s (TCN,DH) segmentation for one total CN segment: 842s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 2 2 1 1 141510003 185449813 2681 2.0689 777 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 842s 2 777 141510003 185449813 777 0.0973 842s Total CN segment #2 ([1.4151e+08,1.8545e+08]) of 3...done 842s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 842s Number of TCN loci in segment: 4391 842s Locus data for TCN segment: 842s 'data.frame': 4391 obs. of 9 variables: 842s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 842s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 842s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 842s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 842s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 842s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 842s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 842s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 842s $ rho : num NA 0.2186 NA 0.0503 NA ... 842s Number of loci: 4391 842s Number of SNPs: 1311 (29.86%) 842s Number of heterozygous SNPs: 1311 (100.00%) 842s Chromosome: 1 842s Segmenting DH signals... 842s Segmenting by CBS... 842s Chromosome: 1 842s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 842s Segmenting by CBS...done 842s List of 4 842s $ data :'data.frame': 4391 obs. of 4 variables: 842s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 842s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 842s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 842s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 842s $ output :'data.frame': 1 obs. of 6 variables: 842s ..$ sampleName: chr NA 842s ..$ chromosome: int 1 842s ..$ start : num 1.85e+08 842s ..$ end : num 2.47e+08 842s ..$ nbrOfLoci : int 1311 842s ..$ mean : num 0.23 842s $ segRows:'data.frame': 1 obs. of 2 variables: 842s ..$ startRow: int 2 842s ..$ endRow : int 4388 842s $ params :List of 5 842s ..$ alpha : num 0.001 842s ..$ undo : num 0 842s ..$ joinSegments : logi TRUE 842s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 842s .. ..$ chromosome: int 1 842s .. ..$ start : num 1.85e+08 842s .. ..$ end : num 2.47e+08 842s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 842s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.049 0 0.048 0 0 842s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 842s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 842s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s DH segmentation (locally-indexed) rows: 842s startRow endRow 842s 1 2 4388 842s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 842s DH segmentation rows: 842s startRow endRow 842s 1 10269 14655 842s Segmenting DH signals...done 842s DH segmentation table: 842s dhStart dhEnd dhNbrOfLoci dhMean 842s 1 185449813 247137334 1311 0.2295 842s startRow endRow 842s 1 10269 14655 842s Rows: 842s [1] 3 842s TCN segmentation rows: 842s startRow endRow 842s 3 10268 14658 842s TCN and DH segmentation rows: 842s startRow endRow 842s 3 10268 14658 842s startRow endRow 842s 1 10269 14655 842s startRow endRow 842s 1 1 7586 842s 2 7587 10267 842s TCN segmentation (expanded) rows: 842s startRow endRow 842s 1 1 7586 842s 2 7587 10267 842s 3 10268 14658 842s TCN and DH segmentation rows: 842s startRow endRow 842s 1 1 7586 842s 2 7587 10267 842s 3 10268 14658 842s startRow endRow 842s 1 10 7574 842s 2 7587 10263 842s 3 10269 14655 842s startRow endRow 842s 1 1 7586 842s 2 7587 10267 842s 3 10268 14658 842s Total CN segmentation table (expanded): 842s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 842s 3 1 185449813 247137334 4391 2.6341 1311 1311 842s (TCN,DH) segmentation for one total CN segment: 842s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 3 3 1 1 185449813 247137334 4391 2.6341 1311 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 842s 3 1311 185449813 247137334 1311 0.2295 842s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 842s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 1 1 1 1 554484 120992603 7586 1.3853 2108 842s 2 1 2 1 141510003 185449813 2681 2.0689 777 842s 3 1 3 1 185449813 247137334 4391 2.6341 1311 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 842s 1 2108 554484 120992603 2108 0.5116 842s 2 777 141510003 185449813 777 0.0973 842s 3 1311 185449813 247137334 1311 0.2295 842s Calculating (C1,C2) per segment... 842s Calculating (C1,C2) per segment...done 842s Number of segments: 3 842s Segmenting paired tumor-normal signals using Paired PSCBS...done 842s Post-segmenting TCNs... 842s Number of segments: 3 842s Number of chromosomes: 1 842s [1] 1 842s Chromosome 1 ('chr01') of 1... 842s Rows: 842s [1] 1 2 3 842s Number of segments: 3 842s TCN segment #1 ('1') of 3... 842s Nothing todo. Only one DH segmentation. Skipping. 842s TCN segment #1 ('1') of 3...done 842s TCN segment #2 ('2') of 3... 842s Nothing todo. Only one DH segmentation. Skipping. 842s TCN segment #2 ('2') of 3...done 842s TCN segment #3 ('3') of 3... 842s Nothing todo. Only one DH segmentation. Skipping. 842s TCN segment #3 ('3') of 3...done 842s Chromosome 1 ('chr01') of 1...done 842s Update (C1,C2) per segment... 842s Update (C1,C2) per segment...done 842s Post-segmenting TCNs...done 842s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 1 1 1 1 554484 120992603 7586 1.3853 2108 842s 2 1 2 1 141510003 185449813 2681 2.0689 777 842s 3 1 3 1 185449813 247137334 4391 2.6341 1311 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 842s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 842s 2 777 141510003 185449813 777 0.0973 0.9337980 1.135102 842s 3 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 842s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 1 1 1 1 554484 120992603 7586 1.3853 2108 842s 2 1 2 1 141510003 185449813 2681 2.0689 777 842s 3 1 3 1 185449813 247137334 4391 2.6341 1311 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 842s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 842s 2 777 141510003 185449813 777 0.0973 0.9337980 1.135102 842s 3 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 842s > print(fit) 842s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 1 1 1 1 554484 120992603 7586 1.3853 2108 842s 2 1 2 1 141510003 185449813 2681 2.0689 777 842s 3 1 3 1 185449813 247137334 4391 2.6341 1311 842s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 842s 1 2108 2108 0.5116 0.3382903 1.047010 842s 2 777 777 0.0973 0.9337980 1.135102 842s 3 1311 1311 0.2295 1.0147870 1.619313 842s > 842s > # Plot results 842s > dev.set(4L) 842s pdf 842s 2 842s > plotTracks(fit) 842s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 842s > 842s > # Sanity check 842s > stopifnot(nbrOfSegments(fit) == nSegs-1L) 842s > 842s > fit3 <- fit 842s > 842s > 842s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 842s > # (d) Skip the identification of new change points 842s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 842s > knownSegments <- data.frame( 842s + chromosome = c( 1, 1), 842s + start = c( -Inf, 141510003), 842s + end = c(120992603, +Inf) 842s + ) 842s > 842s > # Paired PSCBS segmentation 842s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 842s + undoTCN=Inf, undoDH=Inf, 842s + seed=0xBEEF, verbose=-10) 842s Segmenting paired tumor-normal signals using Paired PSCBS... 842s Calling genotypes from normal allele B fractions... 842s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 842s Called genotypes: 842s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 842s - attr(*, "modelFit")=List of 1 842s ..$ :List of 7 842s .. ..$ flavor : chr "density" 842s .. ..$ cn : int 2 842s .. ..$ nbrOfGenotypeGroups: int 3 842s .. ..$ tau : num [1:2] 0.315 0.677 842s .. ..$ n : int 14640 842s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 842s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 842s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 842s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 842s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 842s .. .. ..$ type : chr [1:2] "valley" "valley" 842s .. .. ..$ x : num [1:2] 0.315 0.677 842s .. .. ..$ density: num [1:2] 0.522 0.552 842s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 842s muN 842s 0 0.5 1 842s 5221 4198 5251 842s Calling genotypes from normal allele B fractions...done 842s Normalizing betaT using betaN (TumorBoost)... 842s Normalized BAFs: 842s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 842s - attr(*, "modelFit")=List of 5 842s ..$ method : chr "normalizeTumorBoost" 842s ..$ flavor : chr "v4" 842s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 842s .. ..- attr(*, "modelFit")=List of 1 842s .. .. ..$ :List of 7 842s .. .. .. ..$ flavor : chr "density" 842s .. .. .. ..$ cn : int 2 842s .. .. .. ..$ nbrOfGenotypeGroups: int 3 842s .. .. .. ..$ tau : num [1:2] 0.315 0.677 842s .. .. .. ..$ n : int 14640 842s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 842s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 842s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 842s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 842s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 842s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 842s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 842s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 842s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 842s ..$ preserveScale: logi FALSE 842s ..$ scaleFactor : num NA 842s Normalizing betaT using betaN (TumorBoost)...done 842s Setup up data... 842s 'data.frame': 14670 obs. of 7 variables: 842s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 842s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 842s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 842s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 842s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 842s ..- attr(*, "modelFit")=List of 5 842s .. ..$ method : chr "normalizeTumorBoost" 842s .. ..$ flavor : chr "v4" 842s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 842s .. .. ..- attr(*, "modelFit")=List of 1 842s .. .. .. ..$ :List of 7 842s .. .. .. .. ..$ flavor : chr "density" 842s .. .. .. .. ..$ cn : int 2 842s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 842s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 842s .. .. .. .. ..$ n : int 14640 842s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 842s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 842s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 842s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 842s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 842s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 842s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 842s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 842s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 842s .. ..$ preserveScale: logi FALSE 842s .. ..$ scaleFactor : num NA 842s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 842s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 842s ..- attr(*, "modelFit")=List of 1 842s .. ..$ :List of 7 842s .. .. ..$ flavor : chr "density" 842s .. .. ..$ cn : int 2 842s .. .. ..$ nbrOfGenotypeGroups: int 3 842s .. .. ..$ tau : num [1:2] 0.315 0.677 842s .. .. ..$ n : int 14640 842s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 842s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 842s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 842s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 842s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 842s .. .. .. ..$ type : chr [1:2] "valley" "valley" 842s .. .. .. ..$ x : num [1:2] 0.315 0.677 842s .. .. .. ..$ density: num [1:2] 0.522 0.552 842s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 842s Setup up data...done 842s Dropping loci for which TCNs are missing... 842s Number of loci dropped: 12 842s Dropping loci for which TCNs are missing...done 842s Ordering data along genome... 842s 'data.frame': 14658 obs. of 7 variables: 842s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 842s $ x : num 554484 730720 782343 878522 916294 ... 842s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 842s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 842s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 842s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 842s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 842s Ordering data along genome...done 842s Keeping only current chromosome for 'knownSegments'... 842s Chromosome: 1 842s Known segments for this chromosome: 842s chromosome start end 842s 1 1 -Inf 120992603 842s 2 1 141510003 Inf 842s Keeping only current chromosome for 'knownSegments'...done 842s alphaTCN: 0.009 842s alphaDH: 0.001 842s Number of loci: 14658 842s Calculating DHs... 842s Number of SNPs: 14658 842s Number of heterozygous SNPs: 4196 (28.63%) 842s Normalized DHs: 842s num [1:14658] NA NA NA NA NA ... 842s Calculating DHs...done 842s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 842s Produced 2 seeds from this stream for future usage 842s Identification of change points by total copy numbers... 842s Segmenting by CBS... 842s Chromosome: 1 842s Segmenting multiple segments on current chromosome... 842s Number of segments: 2 842s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 842s Produced 2 seeds from this stream for future usage 842s Segmenting by CBS... 842s Chromosome: 1 842s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 842s Segmenting by CBS...done 842s Segmenting by CBS... 842s Chromosome: 1 842s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 842s Segmenting by CBS...done 842s Segmenting multiple segments on current chromosome...done 842s Segmenting by CBS...done 842s List of 4 842s $ data :'data.frame': 14658 obs. of 4 variables: 842s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 842s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 842s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 842s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 842s $ output :'data.frame': 2 obs. of 6 variables: 842s ..$ sampleName: chr [1:2] NA NA 842s ..$ chromosome: num [1:2] 1 1 842s ..$ start : num [1:2] 5.54e+05 1.42e+08 842s ..$ end : num [1:2] 1.21e+08 2.47e+08 842s ..$ nbrOfLoci : int [1:2] 7586 7072 842s ..$ mean : num [1:2] 1.39 2.42 842s $ segRows:'data.frame': 2 obs. of 2 variables: 842s ..$ startRow: int [1:2] 1 7587 842s ..$ endRow : int [1:2] 7586 14658 842s $ params :List of 7 842s ..$ undo.splits : chr "sdundo" 842s ..$ undo.SD : num Inf 842s ..$ alpha : num 0.009 842s ..$ undo : num Inf 842s ..$ joinSegments : logi TRUE 842s ..$ knownSegments:'data.frame': 2 obs. of 3 variables: 842s .. ..$ chromosome: num [1:2] 1 1 842s .. ..$ start : num [1:2] -Inf 1.42e+08 842s .. ..$ end : num [1:2] 1.21e+08 Inf 842s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 842s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 842s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.009 0 0.009 0 0 842s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 842s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 842s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s Identification of change points by total copy numbers...done 842s Restructure TCN segmentation results... 842s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 842s 1 1 554484 120992603 7586 1.385258 842s 2 1 141510003 247137334 7072 2.419824 842s Number of TCN segments: 2 842s Restructure TCN segmentation results...done 842s Total CN segment #1 ([ 554484,1.20993e+08]) of 2... 842s Number of TCN loci in segment: 7586 842s Locus data for TCN segment: 842s 'data.frame': 7586 obs. of 9 variables: 842s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 842s $ x : num 554484 730720 782343 878522 916294 ... 842s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 842s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 842s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 842s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 842s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 842s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 842s $ rho : num NA NA NA NA NA ... 842s Number of loci: 7586 842s Number of SNPs: 2108 (27.79%) 842s Number of heterozygous SNPs: 2108 (100.00%) 842s Chromosome: 1 842s Segmenting DH signals... 842s Segmenting by CBS... 842s Chromosome: 1 842s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 842s Segmenting by CBS...done 842s List of 4 842s $ data :'data.frame': 7586 obs. of 4 variables: 842s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 842s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 842s ..$ y : num [1:7586] NA NA NA NA NA ... 842s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 842s $ output :'data.frame': 1 obs. of 6 variables: 842s ..$ sampleName: chr NA 842s ..$ chromosome: int 1 842s ..$ start : num 554484 842s ..$ end : num 1.21e+08 842s ..$ nbrOfLoci : int 7586 842s ..$ mean : num 0.512 842s $ segRows:'data.frame': 1 obs. of 2 variables: 842s ..$ startRow: int 1 842s ..$ endRow : int 7586 842s $ params :List of 7 842s ..$ undo.splits : chr "sdundo" 842s ..$ undo.SD : num Inf 842s ..$ alpha : num 0.001 842s ..$ undo : num Inf 842s ..$ joinSegments : logi TRUE 842s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 842s .. ..$ chromosome: int 1 842s .. ..$ start : num 554484 842s .. ..$ end : num 1.21e+08 842s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 842s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.071 0.001 0.072 0 0 842s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 842s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 842s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s DH segmentation (locally-indexed) rows: 842s startRow endRow 842s 1 1 7586 842s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 842s DH segmentation rows: 842s startRow endRow 842s 1 1 7586 842s Segmenting DH signals...done 842s DH segmentation table: 842s dhStart dhEnd dhNbrOfLoci dhMean 842s 1 554484 120992603 7586 0.511612 842s startRow endRow 842s 1 1 7586 842s Rows: 842s [1] 1 842s TCN segmentation rows: 842s startRow endRow 842s 1 1 7586 842s TCN and DH segmentation rows: 842s startRow endRow 842s 1 1 7586 842s startRow endRow 842s 1 1 7586 842s NULL 842s TCN segmentation (expanded) rows: 842s startRow endRow 842s 1 1 7586 842s TCN and DH segmentation rows: 842s startRow endRow 842s 1 1 7586 842s 2 7587 14658 842s startRow endRow 842s 1 1 7586 842s startRow endRow 842s 1 1 7586 842s Total CN segmentation table (expanded): 842s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 842s 1 1 554484 120992603 7586 1.385258 2108 2108 842s (TCN,DH) segmentation for one total CN segment: 842s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 1 1 1 1 554484 120992603 7586 1.385258 2108 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 842s 1 2108 554484 120992603 7586 0.511612 842s Total CN segment #1 ([ 554484,1.20993e+08]) of 2...done 842s Total CN segment #2 ([1.4151e+08,2.47137e+08]) of 2... 842s Number of TCN loci in segment: 7072 842s Locus data for TCN segment: 842s 'data.frame': 7072 obs. of 9 variables: 842s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 842s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 842s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 842s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 842s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 842s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 842s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 842s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 842s $ rho : num 0.117 0.258 NA NA NA ... 842s Number of loci: 7072 842s Number of SNPs: 2088 (29.52%) 842s Number of heterozygous SNPs: 2088 (100.00%) 842s Chromosome: 1 842s Segmenting DH signals... 842s Segmenting by CBS... 842s Chromosome: 1 842s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 842s Segmenting by CBS...done 842s List of 4 842s $ data :'data.frame': 7072 obs. of 4 variables: 842s ..$ chromosome: int [1:7072] 1 1 1 1 1 1 1 1 1 1 ... 842s ..$ x : num [1:7072] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 842s ..$ y : num [1:7072] 0.117 0.258 NA NA NA ... 842s ..$ index : int [1:7072] 1 2 3 4 5 6 7 8 9 10 ... 842s $ output :'data.frame': 1 obs. of 6 variables: 842s ..$ sampleName: chr NA 842s ..$ chromosome: int 1 842s ..$ start : num 1.42e+08 842s ..$ end : num 2.47e+08 842s ..$ nbrOfLoci : int 7072 842s ..$ mean : num 0.18 842s $ segRows:'data.frame': 1 obs. of 2 variables: 842s ..$ startRow: int 1 842s ..$ endRow : int 7072 842s $ params :List of 7 842s ..$ undo.splits : chr "sdundo" 842s ..$ undo.SD : num Inf 842s ..$ alpha : num 0.001 842s ..$ undo : num Inf 842s ..$ joinSegments : logi TRUE 842s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 842s .. ..$ chromosome: int 1 842s .. ..$ start : num 1.42e+08 842s .. ..$ end : num 2.47e+08 842s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 842s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.016 0 0.016 0 0 842s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 842s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 842s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 842s DH segmentation (locally-indexed) rows: 842s startRow endRow 842s 1 1 7072 842s int [1:7072] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 842s DH segmentation rows: 842s startRow endRow 842s 1 7587 14658 842s Segmenting DH signals...done 842s DH segmentation table: 842s dhStart dhEnd dhNbrOfLoci dhMean 842s 1 141510003 247137334 7072 0.1803011 842s startRow endRow 842s 1 7587 14658 842s Rows: 842s [1] 2 842s TCN segmentation rows: 842s startRow endRow 842s 2 7587 14658 842s TCN and DH segmentation rows: 842s startRow endRow 842s 2 7587 14658 842s startRow endRow 842s 1 7587 14658 842s startRow endRow 842s 1 1 7586 842s TCN segmentation (expanded) rows: 842s startRow endRow 842s 1 1 7586 842s 2 7587 14658 842s TCN and DH segmentation rows: 842s startRow endRow 842s 1 1 7586 842s 2 7587 14658 842s startRow endRow 842s 1 1 7586 842s 2 7587 14658 842s startRow endRow 842s 1 1 7586 842s 2 7587 14658 842s Total CN segmentation table (expanded): 842s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 2 1 141510003 247137334 7072 2.419824 2088 842s tcnNbrOfHets 842s 2 2088 842s (TCN,DH) segmentation for one total CN segment: 842s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 2 2 1 1 141510003 247137334 7072 2.419824 2088 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 842s 2 2088 141510003 247137334 7072 0.1803011 842s Total CN segment #2 ([1.4151e+08,2.47137e+08]) of 2...done 842s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 1 1 1 1 554484 120992603 7586 1.385258 2108 842s 2 1 2 1 141510003 247137334 7072 2.419824 2088 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 842s 1 2108 554484 120992603 7586 0.5116120 842s 2 2088 141510003 247137334 7072 0.1803011 842s Calculating (C1,C2) per segment... 842s Calculating (C1,C2) per segment...done 842s Number of segments: 2 842s Segmenting paired tumor-normal signals using Paired PSCBS...done 842s Post-segmenting TCNs... 842s Number of segments: 2 842s Number of chromosomes: 1 842s [1] 1 842s Chromosome 1 ('chr01') of 1... 842s Rows: 842s [1] 1 2 842s Number of segments: 2 842s TCN segment #1 ('1') of 2... 842s Nothing todo. Only one DH segmentation. Skipping. 842s TCN segment #1 ('1') of 2...done 842s TCN segment #2 ('2') of 2... 842s Nothing todo. Only one DH segmentation. Skipping. 842s TCN segment #2 ('2') of 2...done 842s Chromosome 1 ('chr01') of 1...done 842s Update (C1,C2) per segment... 842s Update (C1,C2) per segment...done 842s Post-segmenting TCNs...done 842s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 1 1 1 1 554484 120992603 7586 1.385258 2108 842s 2 1 2 1 141510003 247137334 7072 2.419824 2088 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 842s 1 2108 554484 120992603 7586 0.5116120 0.3382717 1.046986 842s 2 2088 141510003 247137334 7072 0.1803011 0.9917635 1.428060 842s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 1 1 1 1 554484 120992603 7586 1.385258 2108 842s 2 1 2 1 141510003 247137334 7072 2.419824 2088 842s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 842s 1 2108 554484 120992603 7586 0.5116120 0.3382717 1.046986 842s 2 2088 141510003 247137334 7072 0.1803011 0.9917635 1.428060 842s > print(fit) 842s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 842s 1 1 1 1 554484 120992603 7586 1.385258 2108 842s 2 1 2 1 141510003 247137334 7072 2.419824 2088 842s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 842s 1 2108 7586 0.5116120 0.3382717 1.046986 842s 2 2088 7072 0.1803011 0.9917635 1.428060 842s > 842s > # Plot results 842s > dev.set(5L) 842s pdf 842s 2 842s > plotTracks(fit) 842s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 842s > 842s > # Sanity check 842s > stopifnot(nbrOfSegments(fit) == nrow(knownSegments)) 842s > 842s > fit4 <- fit 842s > 842s > 842s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 842s > # Tiling multiple chromosomes 842s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 842s > # Simulate multiple chromosomes 842s > fit1 <- fit 842s > fit2 <- renameChromosomes(fit, from=1, to=2) 842s > fitM <- c(fit1, fit2) 842s > 842s > # Tile chromosomes 842s > fitT <- tileChromosomes(fitM) 842s > fitTb <- tileChromosomes(fitT) 842s > stopifnot(identical(fitTb, fitT)) 842s > 842s > # Plotting multiple chromosomes 842s > plotTracks(fitT) 842s > 842s > proc.time() 842s user system elapsed 842s 36.012 1.046 37.134 842s Test segmentByPairedPSCBS passed 842s 0 842s Begin test weightedQuantile 842s + [ 0 != 0 ] 842s + echo Test segmentByPairedPSCBS passed 842s + echo 0 842s + echo Begin test weightedQuantile 842s + exitcode=0 842s + R CMD BATCH weightedQuantile.R 858s + cat weightedQuantile.Rout 858s 858s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 858s Copyright (C) 2024 The R Foundation for Statistical Computing 858s Platform: aarch64-unknown-linux-gnu (64-bit) 858s 858s R is free software and comes with ABSOLUTELY NO WARRANTY. 858s You are welcome to redistribute it under certain conditions. 858s Type 'license()' or 'licence()' for distribution details. 858s 858s R is a collaborative project with many contributors. 858s Type 'contributors()' for more information and 858s 'citation()' on how to cite R or R packages in publications. 858s 858s Type 'demo()' for some demos, 'help()' for on-line help, or 858s 'help.start()' for an HTML browser interface to help. 858s Type 'q()' to quit R. 858s 858s [Previously saved workspace restored] 858s 858s > library("PSCBS") 858s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 858s 858s Attaching package: 'PSCBS' 858s 858s The following objects are masked from 'package:base': 858s 858s append, load 858s 858s > library("stats") 858s > 858s > message("weightedQuantile() ...") 858s weightedQuantile() ... 858s > 858s > if (requireNamespace("Hmisc")) { 858s + message(" - assert identical results to Hmisc::wtd.quantile()") 858s + wtd.quantile <- Hmisc::wtd.quantile 858s + for (kk in 1:100) { 858s + n <- 5L + sample.int(995, size = 1L) 858s + x <- rnorm(n, mean = 0.0, sd = 1.0) 858s + w <- runif(n, min = 0.5, max = 2.0) ## Non-normalized weights 858s + probs <- c(0.0, 0.25, 0.50, 0.75, 1.0) 858s + q0 <- wtd.quantile(x, weights = w, probs = probs, normwt = TRUE) 858s + q <- weightedQuantile(x, w = w, probs = probs) 858s + if (!isTRUE(all.equal(q, q0))) { 858s + print(q0) 858s + print(q) 858s + stopifnot(all.equal(q, q0)) 858s + } 858s + } 858s + } 858s Loading required namespace: Hmisc 858s - assert identical results to Hmisc::wtd.quantile() 858s > 858s > message("weightedQuantile() ... DONE") 858s weightedQuantile() ... DONE 858s > 858s > proc.time() 858s user system elapsed 858s 10.681 1.166 11.802 858s + [ 0 !=Test weightedQuantile passed 858s 0 858s 0 ] 858s + echo Test weightedQuantile passed 858s + echo 0 858s + rm -f /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/PairedPSCBS,boot.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/PairedPSCBS,boot.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/Rplots.pdf /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/findLargeGaps.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/findLargeGaps.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/randomSeed.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/randomSeed.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByCBS,calls.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByCBS,calls.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByCBS,futures.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByCBS,futures.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByCBS,median.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByCBS,median.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByCBS,prune.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByCBS,prune.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByCBS,report.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByCBS,report.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByCBS,shiftTCN.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByCBS,shiftTCN.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByCBS,weights.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByCBS,weights.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByCBS.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByCBS.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByNonPairedPSCBS,medianDH.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByNonPairedPSCBS,medianDH.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByPairedPSCBS,DH.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByPairedPSCBS,DH.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByPairedPSCBS,calls.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByPairedPSCBS,calls.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByPairedPSCBS,futures.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByPairedPSCBS,futures.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByPairedPSCBS,noNormalBAFs.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByPairedPSCBS,noNormalBAFs.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByPairedPSCBS,report.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByPairedPSCBS,report.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByPairedPSCBS,seqOfSegmentsByDP.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByPairedPSCBS,seqOfSegmentsByDP.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByPairedPSCBS.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/segmentByPairedPSCBS.Rout /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/weightedQuantile.R /tmp/autopkgtest.H7uPRv/autopkgtest_tmp/weightedQuantile.Rout 859s autopkgtest [19:51:30]: test run-unit-test: -----------------------] 860s run-unit-test PASS 860s autopkgtest [19:51:31]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 861s autopkgtest [19:51:32]: @@@@@@@@@@@@@@@@@@@@ summary 861s run-unit-test PASS 890s Creating nova instance adt-noble-arm64-r-cran-pscbs-20240316-193711-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240316.img (UUID 9d2e92bf-2787-45c2-ae22-99fb4bcc175e)...