Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1626/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
QDNAseq 1.42.0 (landing page) Daoud Sie
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the QDNAseq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/QDNAseq.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: QDNAseq |
Version: 1.42.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:QDNAseq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings QDNAseq_1.42.0.tar.gz |
StartedAt: 2024-11-20 07:52:25 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 07:58:41 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 375.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: QDNAseq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:QDNAseq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings QDNAseq_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/QDNAseq.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘QDNAseq/DESCRIPTION’ ... OK * this is package ‘QDNAseq’ version ‘1.42.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘QDNAseq’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed callBins 16.398 0.148 19.075 frequencyPlot 15.709 0.012 18.006 normalizeSegmentedBins 5.286 0.004 6.446 segmentBins 5.180 0.007 6.576 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘QDNAseq,copyneutral.R’ Running ‘QDNAseq,gain-copyneutral-gain.R’ Running ‘QDNAseq,parallel-reproducibility.R’ Running ‘QDNAseq.R’ Running ‘binReadCounts.R’ Running ‘poolRuns.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
QDNAseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL QDNAseq ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘QDNAseq’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (QDNAseq)
QDNAseq.Rcheck/tests/binReadCounts.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(QDNAseq) > > if (requireNamespace("QDNAseq.hg19", quietly = TRUE)) { + bins <- getBinAnnotations(500, genome = "hg19") + print(bins) + + bam <- system.file("extdata", "ex1.bam", package = "Rsamtools") + print(bam) + + counts <- binReadCounts(bins, bamfiles = bam) + print(counts) + + ## BUG: https://github.com/ccagc/QDNAseq/issues/89 + counts2 <- binReadCounts(bins, bamfiles = bam, chunkSize = 10e3) + print(counts2) + } Loaded bin annotations for genome 'hg19', bin size 500 kbp, and experiment type 'SR50' from annotation package QDNAseq.hg19 v1.36.0 QDNAseq bin annotations for Hsapiens, build hg19. Created by Ilari Scheinin with QDNAseq 0.7.5, 2014-02-06 09:20:46.041402. An object of class 'AnnotatedDataFrame' rowNames: 1:1-500000 1:500001-1000000 ... Y:59000001-59373566 (6206 total) varLabels: chromosome start ... use (9 total) varMetadata: labelDescription [1] "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rsamtools/extdata/ex1.bam" ex1 (1 of 1): extracting reads ... binning ... QDNAseqReadCounts (storageMode: lockedEnvironment) assayData: 6206 features, 1 samples element names: counts protocolData: none phenoData sampleNames: ex1 varLabels: name total.reads used.reads expected.variance varMetadata: labelDescription featureData featureNames: 1:1-500000 1:500001-1000000 ... Y:59000001-59373566 (6206 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: ex1 (1 of 1): extracting reads ... binning chunk - seq1:1:10001 binning chunk - seq2:1:10001 QDNAseqReadCounts (storageMode: lockedEnvironment) assayData: 6206 features, 1 samples element names: counts protocolData: none phenoData sampleNames: ex1 varLabels: name total.reads used.reads expected.variance varMetadata: labelDescription featureData featureNames: 1:1-500000 1:500001-1000000 ... Y:59000001-59373566 (6206 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > > > > proc.time() user system elapsed 5.013 0.325 5.700
QDNAseq.Rcheck/tests/poolRuns.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(QDNAseq) > library(Biobase) ## sampleNames() Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > > data(LGG150) > > message("poolRuns(LGG150) ...") poolRuns(LGG150) ... > pooledReadCounts <- poolRuns(LGG150, samples = sampleNames(LGG150)) > print(pooledReadCounts) QDNAseqReadCounts (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: counts protocolData: none phenoData sampleNames: LGG150 varLabels: name reads used.reads expected.variance varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > message("poolRuns(LGG150) ... done") poolRuns(LGG150) ... done > > > message("Create fake data set with two samples ...") Create fake data set with two samples ... > phenodata <- phenoData(LGG150) > phenodata@data <- rbind(phenodata@data, phenodata@data) > > counts <- assayDataElement(LGG150, "counts") > counts2 <- cbind(counts, counts) > colnames(counts2) <- sampleNames(phenodata) > > x <- new("QDNAseqReadCounts", bins = featureData(LGG150), phenodata = phenodata, counts = counts2) > print(x) QDNAseqReadCounts (storageMode: lockedEnvironment) assayData: 38819 features, 2 samples element names: counts protocolData: none phenoData sampleNames: LGG150 LGG1501 varLabels: name reads used.reads expected.variance varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > message("Create fake data set with two samples ... done") Create fake data set with two samples ... done > > message("poolRuns(LGG150set) ...") poolRuns(LGG150set) ... > x_pool <- poolRuns(x, samples = sampleNames(x)) > print(x_pool) QDNAseqReadCounts (storageMode: lockedEnvironment) assayData: 38819 features, 2 samples element names: counts protocolData: none phenoData sampleNames: LGG150 LGG1501 varLabels: name reads used.reads expected.variance varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > > message("poolRuns(LGG150set) - pooled ...") poolRuns(LGG150set) - pooled ... > ## BUG #112 (https://github.com/ccagc/QDNAseq/issues/112) > x_pool <- poolRuns(x, samples = rep("pooled", times = 2L)) > print(x_pool) QDNAseqReadCounts (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: counts protocolData: none phenoData sampleNames: pooled varLabels: name reads ... total.reads (5 total) varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > > message("poolRuns(LGG150set) ... done") poolRuns(LGG150set) ... done > > proc.time() user system elapsed 3.342 0.284 3.753
QDNAseq.Rcheck/tests/QDNAseq,copyneutral.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(QDNAseq) > library(Biobase) Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > set.seed(0xBEEF) > > data(LGG150) > data <- LGG150 > print(data) QDNAseqReadCounts (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: counts protocolData: none phenoData sampleNames: LGG150 varLabels: name reads used.reads expected.variance varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > > dataF <- applyFilters(data, residual=TRUE, blacklist=TRUE) 38,819 total bins 38,819 of which in selected chromosomes 36,722 of which with reference sequence 33,347 final bins > print(dataF) QDNAseqReadCounts (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: counts protocolData: none phenoData sampleNames: LGG150 varLabels: name reads used.reads expected.variance varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > > dataC <- correctBins(dataF) Calculating correction for GC content and mappability Calculating fit for sample LGG150 (1 of 1) ... Done. > > ## Force all copy neutral data > cn <- assayDataElement(dataC, "copynumber") > cn[,1] <- rnorm(nrow(cn), mean = 1.0, sd = 0.05) > assayDataElement(dataC, "copynumber") <- cn > > print(dataC) QDNAseqCopyNumbers (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: copynumber protocolData: none phenoData sampleNames: LGG150 varLabels: name reads ... loess.family (6 total) varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > > dataN <- normalizeBins(dataC) Applying median normalization ... > print(dataN) QDNAseqCopyNumbers (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: copynumber protocolData: none phenoData sampleNames: LGG150 varLabels: name reads ... loess.family (6 total) varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > > fit <- segmentBins(dataN) Performing segmentation: Segmenting: LGG150 (1 of 1) ... > print(fit) QDNAseqCopyNumbers (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: copynumber, segmented protocolData: none phenoData sampleNames: LGG150 varLabels: name reads ... loess.family (6 total) varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > > fitC <- callBins(fit) EM algorithm started ... [1] "Total number of segments present in the data: 4" [1] "Number of segments used for fitting the model: 4" 38968128033081208.261.3770484214957129411.5114.2770484210264672411.578.4 Calling iteration1: optim results time: 0 minimum: 16682.0890247004 116682.0890247004-0.825303675797091-0.323169506423803-0.001754401929814960.2970863141060160.5078724084702190.9928769615298530.1100346090918040.0003692713871108020.0111811691191362-0.0001065348234756080.1102701734224670.145866377811007 38983178036502208.261.4770484214957129411.5114.2770484210264672411.578.4 Calling iteration2: optim results time: 0 minimum: 16682.0888522346 116682.0888522346-0.816384144994661-0.31848916294222-0.00167850977268490.292952991143050.5008064461942260.9819310567480430.1311557982956840.0002223141320088620.01118096583020170.0001872099918784220.1313921659017140.175722206269368 EM algorithm done ... Computing posterior probabilities for all segments ... Total time:0minutes Adjusting segmented data for cellularity ... Cellularity sample1: 1 Adjusting normalized data for cellularity ... Cellularity sample1: 1 1 39009858258256208.463.1770484214957129411.5114.2770484210774633411.582.3 39010048425002208.464.3770484214957129411.5114.2770484210774633411.582.3 39010018424996208.464.3770484214957129411.5114.2770484210774633411.582.3 39010298691776208.466.4770484214957129411.5114.2770484210774633411.582.3 39014468692710208.466.4770484214957129411.5114.2770484210774633411.582.3 39014558692714208.466.4770484214957129411.5114.2770484210774633411.582.3 39014648692718208.466.4770484214957129411.5114.2770484210774633411.582.3 39014738692722208.466.4770484214957129411.5114.2770484210774633411.582.3 39014828692726208.466.4770484214957129411.5114.2770484210774633411.582.3 39014888692729208.466.4770484214957129411.5114.2770484210774633411.582.3 39015078759459208.466.9770484214957129411.5114.2770484210774633411.582.3 39019248759839208.466.9770484214957129411.5114.2770484210774633411.582.3 FINISHED! Total time:0minutes There were 24 warnings (use warnings() to see them) > print(fitC) QDNAseqCopyNumbers (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: calls, copynumber, probamp, probdloss, probgain, probloss, probnorm, segmented protocolData: none phenoData sampleNames: LGG150 varLabels: name reads ... loess.family (6 total) varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > > > ## Assert that everything is called copy-neutral > calls <- assayDataElement(fitC, "calls") > stopifnot(all(is.na(calls) | calls == 0)) > > formats <- c("tsv", "igv", "bed", "seg", "vcf") > types <- c("copynumber", "segments", "calls") > for (format in formats) { + for (type in types) { + fileext <- sprintf(".%s.%s", type, format) + file <- tempfile(pattern = "QDNAseq-%s", fileext = fileext) + message(sprintf(" - exportBins(<%d samples>, format=\"%s\", type=\"%s\")", ncol(fitC), format, type)) + file <- exportBins(fitC, format = format, type = type, file = file) + message(sprintf(" File(s) written: [n=%d] %s", + length(file), paste(sQuote(file), collapse = ", "))) + stopifnot(all(file_test("-f", file))) + if (format == "seg") { + segs <- read.table(file, sep = "\t", header = TRUE) + print(segs) + stopifnot(nrow(segs) == 0L) + } else if (format == "vcf") { + rows <- readLines(file) + rows <- grep("^#", rows, invert = TRUE, value = TRUE) + print(rows) + stopifnot(length(rows) == 0L) + } + file.remove(file) + stopifnot(!any(file_test("-f", file))) + } + } - exportBins(<1 samples>, format="tsv", type="copynumber") File(s) written: [n=1] '/tmp/Rtmp0gMOYP/QDNAseq-%s17fa5d711d729.copynumber.tsv' - exportBins(<1 samples>, format="tsv", type="segments") File(s) written: [n=1] '/tmp/Rtmp0gMOYP/QDNAseq-%s17fa5de288d89.segments.tsv' - exportBins(<1 samples>, format="tsv", type="calls") File(s) written: [n=1] '/tmp/Rtmp0gMOYP/QDNAseq-%s17fa5d291ce6e6.calls.tsv' - exportBins(<1 samples>, format="igv", type="copynumber") File(s) written: [n=1] '/tmp/Rtmp0gMOYP/QDNAseq-%s17fa5d59b6dfca.copynumber.igv' - exportBins(<1 samples>, format="igv", type="segments") File(s) written: [n=1] '/tmp/Rtmp0gMOYP/QDNAseq-%s17fa5d6489f26b.segments.igv' - exportBins(<1 samples>, format="igv", type="calls") File(s) written: [n=1] '/tmp/Rtmp0gMOYP/QDNAseq-%s17fa5d314fcb8.calls.igv' - exportBins(<1 samples>, format="bed", type="copynumber") File(s) written: [n=1] '/tmp/Rtmp0gMOYP/QDNAseq-LGG15017fa5d69e40019.copynumber.bed' - exportBins(<1 samples>, format="bed", type="segments") File(s) written: [n=1] '/tmp/Rtmp0gMOYP/QDNAseq-LGG15017fa5d48eaee62.segments.bed' - exportBins(<1 samples>, format="bed", type="calls") File(s) written: [n=1] '/tmp/Rtmp0gMOYP/QDNAseq-LGG15017fa5d7fed96c8.calls.bed' - exportBins(<1 samples>, format="seg", type="copynumber") File(s) written: [n=1] '/tmp/Rtmp0gMOYP/QDNAseq-LGG15017fa5d7051a350.copynumber.seg' [1] SAMPLE_NAME CHROMOSOME START STOP [5] DATAPOINTS LOG2_RATIO_MEAN <0 rows> (or 0-length row.names) - exportBins(<1 samples>, format="seg", type="segments") File(s) written: [n=1] '/tmp/Rtmp0gMOYP/QDNAseq-LGG15017fa5d167eba5c.segments.seg' [1] SAMPLE_NAME CHROMOSOME START STOP [5] DATAPOINTS LOG2_RATIO_MEAN <0 rows> (or 0-length row.names) - exportBins(<1 samples>, format="seg", type="calls") File(s) written: [n=1] '/tmp/Rtmp0gMOYP/QDNAseq-LGG15017fa5d5993aecc.calls.seg' [1] SAMPLE_NAME CHROMOSOME START STOP [5] DATAPOINTS LOG2_RATIO_MEAN <0 rows> (or 0-length row.names) - exportBins(<1 samples>, format="vcf", type="copynumber") File(s) written: [n=1] '/tmp/Rtmp0gMOYP/QDNAseq-LGG15017fa5d469732e.copynumber.vcf' character(0) - exportBins(<1 samples>, format="vcf", type="segments") File(s) written: [n=1] '/tmp/Rtmp0gMOYP/QDNAseq-LGG15017fa5d53da0317.segments.vcf' character(0) - exportBins(<1 samples>, format="vcf", type="calls") File(s) written: [n=1] '/tmp/Rtmp0gMOYP/QDNAseq-LGG15017fa5d717d82ed.calls.vcf' character(0) > > proc.time() user system elapsed 15.912 0.456 19.609
QDNAseq.Rcheck/tests/QDNAseq,gain-copyneutral-gain.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(QDNAseq) > library(Biobase) Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > library(utils) > set.seed(0xBEEF) > > data(LGG150) > data <- LGG150 > print(data) QDNAseqReadCounts (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: counts protocolData: none phenoData sampleNames: LGG150 varLabels: name reads used.reads expected.variance varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > > dataF <- applyFilters(data, residual=TRUE, blacklist=TRUE) 38,819 total bins 38,819 of which in selected chromosomes 36,722 of which with reference sequence 33,347 final bins > print(dataF) QDNAseqReadCounts (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: counts protocolData: none phenoData sampleNames: LGG150 varLabels: name reads used.reads expected.variance varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > > dataC <- correctBins(dataF) Calculating correction for GC content and mappability Calculating fit for sample LGG150 (1 of 1) ... Done. > > ## Force results to have segments gain, copy neutral, and gain. > cnAll <- assayDataElement(dataC, "copynumber") > cnAll[,1] <- rnorm(nrow(cnAll), mean = 1.0, sd = 0.05) > chr7 <- (chromosomes(dataC) == "7") > cn <- cnAll[chr7, , drop = FALSE] > n <- nrow(cn) > idxs <- seq(from=1/3*n - 0.1*n, to=1/3*n + 0.1*n) > cn[idxs,1] <- rnorm(length(idxs), mean = 2.0, sd = 0.05) > idxs <- seq(from=2/3*n - 0.1*n, to=2/3*n + 0.1*n) > cn[idxs,1] <- rnorm(length(idxs), mean = 2.0, sd = 0.05) > cnAll[chr7, ] <- cn > assayDataElement(dataC, "copynumber") <- cnAll > print(dataC) QDNAseqCopyNumbers (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: copynumber protocolData: none phenoData sampleNames: LGG150 varLabels: name reads ... loess.family (6 total) varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > > dataN <- normalizeBins(dataC) Applying median normalization ... > print(dataN) QDNAseqCopyNumbers (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: copynumber protocolData: none phenoData sampleNames: LGG150 varLabels: name reads ... loess.family (6 total) varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > > fit <- segmentBins(dataN) Performing segmentation: Segmenting: LGG150 (1 of 1) ... > print(fit) QDNAseqCopyNumbers (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: copynumber, segmented protocolData: none phenoData sampleNames: LGG150 varLabels: name reads ... loess.family (6 total) varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > > fitC <- callBins(fit) EM algorithm started ... [1] "Total number of segments present in the data: 8" [1] "Number of segments used for fitting the model: 8" 38971228076660208.261.7770484214957129411.5114.2770484210264672411.578.4 Calling iteration1: optim results time: 0 minimum: 16691.936015802 116691.936015802-0.76889026698241-0.310183146024425-0.01185150972096230.2885943760685340.4933553445096880.9879385470392230.0299884700901994-0.0005485736219481460.0111821966975442-4.08995447325668e-050.01000052582656670.0100005260086061 EM algorithm done ... Computing posterior probabilities for all segments ... Total time:0minutes Adjusting segmented data for cellularity ... Cellularity sample1: 1 Adjusting normalized data for cellularity ... Cellularity sample1: 1 1 39012958301643208.463.4770484214957129411.5114.2770484210818339411.582.6 39013148468389208.464.7770484214957129411.5114.2770484210818339411.582.6 39013118468383208.464.7770484214957129411.5114.2770484210818339411.582.6 39013398736913208.466.7770484214957129411.5114.2770484210818339411.582.6 39017568737847208.466.7770484214957129411.5114.2770484210818339411.582.6 39017658737851208.466.7770484214957129411.5114.2770484210818339411.582.6 39017748737855208.466.7770484214957129411.5114.2770484210818339411.582.6 39017838737859208.466.7770484214957129411.5114.2770484210818339411.582.6 39017928737863208.466.7770484214957129411.5114.2770484210818339411.582.6 39017988737866208.466.7770484214957129411.5114.2770484210818339411.582.6 39018178804596208.467.2770484218028554411.5137.6770484210818339411.582.6 39022348804976208.567.2770484218028554411.5137.6770484210818339411.582.6 FINISHED! Total time:0minutes There were 32 warnings (use warnings() to see them) > print(fitC) QDNAseqCopyNumbers (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: calls, copynumber, probamp, probdloss, probgain, probloss, probnorm, segmented protocolData: none phenoData sampleNames: LGG150 varLabels: name reads ... loess.family (6 total) varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > > ## Assert that everything is called copy-neutral > calls <- assayDataElement(fitC, "calls") > stopifnot(all(is.na(calls) | calls %in% c(0, 2))) > > formats <- c("tsv", "igv", "bed", "seg", "vcf") > types <- c("copynumber", "segments", "calls") > for (format in formats) { + for (type in types) { + fileext <- sprintf(".%s.%s", type, format) + file <- tempfile(pattern = "QDNAseq-%s", fileext = fileext) + message(sprintf(" - exportBins(<%d samples>, format=\"%s\", type=\"%s\")", ncol(fitC), format, type)) + file <- exportBins(fitC, format = format, type = type, file = file) + message(sprintf(" File(s) written: [n=%d] %s", + length(file), paste(sQuote(file), collapse = ", "))) + stopifnot(all(file_test("-f", file))) + + if (format == "seg") { + segs <- read.table(file, sep = "\t", header = TRUE) + print(segs) + stopifnot(all(segs$CHROMOSOME == "7"), nrow(segs) == 2L) + } else if (format == "vcf") { + segs <- read.table(file, sep = "\t", header = FALSE) + print(segs) + stopifnot(all(segs$V1 == "7"), nrow(segs) == 2L) + } + + file.remove(file) + stopifnot(!any(file_test("-f", file))) + } + } - exportBins(<1 samples>, format="tsv", type="copynumber") File(s) written: [n=1] '/tmp/Rtmp12xOtV/QDNAseq-%s17fde8159cd94.copynumber.tsv' - exportBins(<1 samples>, format="tsv", type="segments") File(s) written: [n=1] '/tmp/Rtmp12xOtV/QDNAseq-%s17fde8e3f24d1.segments.tsv' - exportBins(<1 samples>, format="tsv", type="calls") File(s) written: [n=1] '/tmp/Rtmp12xOtV/QDNAseq-%s17fde81810d57f.calls.tsv' - exportBins(<1 samples>, format="igv", type="copynumber") File(s) written: [n=1] '/tmp/Rtmp12xOtV/QDNAseq-%s17fde817d11ed1.copynumber.igv' - exportBins(<1 samples>, format="igv", type="segments") File(s) written: [n=1] '/tmp/Rtmp12xOtV/QDNAseq-%s17fde81e46a5aa.segments.igv' - exportBins(<1 samples>, format="igv", type="calls") File(s) written: [n=1] '/tmp/Rtmp12xOtV/QDNAseq-%s17fde83910b185.calls.igv' - exportBins(<1 samples>, format="bed", type="copynumber") File(s) written: [n=1] '/tmp/Rtmp12xOtV/QDNAseq-LGG15017fde84aa4158d.copynumber.bed' - exportBins(<1 samples>, format="bed", type="segments") File(s) written: [n=1] '/tmp/Rtmp12xOtV/QDNAseq-LGG15017fde81b5d2093.segments.bed' - exportBins(<1 samples>, format="bed", type="calls") File(s) written: [n=1] '/tmp/Rtmp12xOtV/QDNAseq-LGG15017fde8533fcc39.calls.bed' - exportBins(<1 samples>, format="seg", type="copynumber") File(s) written: [n=1] '/tmp/Rtmp12xOtV/QDNAseq-LGG15017fde8498eb20f.copynumber.seg' SAMPLE_NAME CHROMOSOME 1 /tmp/Rtmp12xOtV/QDNAseq-LGG15017fde8498eb20f.copynumber.seg 7 2 /tmp/Rtmp12xOtV/QDNAseq-LGG15017fde8498eb20f.copynumber.seg 7 START STOP DATAPOINTS LOG2_RATIO_MEAN 1 37110001 68955000 1487 0.99 2 90165001 122010000 2012 0.99 - exportBins(<1 samples>, format="seg", type="segments") File(s) written: [n=1] '/tmp/Rtmp12xOtV/QDNAseq-LGG15017fde81a750786.segments.seg' SAMPLE_NAME CHROMOSOME START 1 /tmp/Rtmp12xOtV/QDNAseq-LGG15017fde81a750786.segments.seg 7 37110001 2 /tmp/Rtmp12xOtV/QDNAseq-LGG15017fde81a750786.segments.seg 7 90165001 STOP DATAPOINTS LOG2_RATIO_MEAN 1 68955000 1487 0.99 2 122010000 2012 0.99 - exportBins(<1 samples>, format="seg", type="calls") File(s) written: [n=1] '/tmp/Rtmp12xOtV/QDNAseq-LGG15017fde8798d2b6f.calls.seg' SAMPLE_NAME CHROMOSOME START 1 /tmp/Rtmp12xOtV/QDNAseq-LGG15017fde8798d2b6f.calls.seg 7 37110001 2 /tmp/Rtmp12xOtV/QDNAseq-LGG15017fde8798d2b6f.calls.seg 7 90165001 STOP DATAPOINTS LOG2_RATIO_MEAN 1 68955000 1487 0.99 2 122010000 2012 0.99 - exportBins(<1 samples>, format="vcf", type="copynumber") File(s) written: [n=1] '/tmp/Rtmp12xOtV/QDNAseq-LGG15017fde842cd9e50.copynumber.vcf' V1 V2 V3 V4 V5 V6 V7 1 7 37110001 . <DIP> <DUP> 1000 PASS 2 7 90165001 . <DIP> <DUP> 1000 PASS V8 V9 V10 1 SVTYPE=DUP;END=68955000;SVLEN=31845000;BINS=1487;SCORE=2;LOG2CNT=0.99 GT 0/1 2 SVTYPE=DUP;END=122010000;SVLEN=31845000;BINS=2012;SCORE=2;LOG2CNT=0.99 GT 0/1 - exportBins(<1 samples>, format="vcf", type="segments") File(s) written: [n=1] '/tmp/Rtmp12xOtV/QDNAseq-LGG15017fde84b9541de.segments.vcf' V1 V2 V3 V4 V5 V6 V7 1 7 37110001 . <DIP> <DUP> 1000 PASS 2 7 90165001 . <DIP> <DUP> 1000 PASS V8 V9 V10 1 SVTYPE=DUP;END=68955000;SVLEN=31845000;BINS=1487;SCORE=2;LOG2CNT=0.99 GT 0/1 2 SVTYPE=DUP;END=122010000;SVLEN=31845000;BINS=2012;SCORE=2;LOG2CNT=0.99 GT 0/1 - exportBins(<1 samples>, format="vcf", type="calls") File(s) written: [n=1] '/tmp/Rtmp12xOtV/QDNAseq-LGG15017fde81b8f53c3.calls.vcf' V1 V2 V3 V4 V5 V6 V7 1 7 37110001 . <DIP> <DUP> 1000 PASS 2 7 90165001 . <DIP> <DUP> 1000 PASS V8 V9 V10 1 SVTYPE=DUP;END=68955000;SVLEN=31845000;BINS=1487;SCORE=2;LOG2CNT=0.99 GT 0/1 2 SVTYPE=DUP;END=122010000;SVLEN=31845000;BINS=2012;SCORE=2;LOG2CNT=0.99 GT 0/1 > > proc.time() user system elapsed 15.570 0.447 17.647
QDNAseq.Rcheck/tests/QDNAseq,parallel-reproducibility.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > ###################################################################### > # This scripts asserts that for each processing step of QDNAseq > # the output/results are reproducible (numerically equal). > ###################################################################### > library("QDNAseq") > options("QDNAseq::verbose"=FALSE) > > # Load data > data(LGG150) > data <- LGG150 > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # TRUTH > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Filter out "bad" bins > dataF <- applyFilters(data, residual=TRUE, blacklist=TRUE) > > # Correct read counts as a function of GC content and mappability > dataC <- correctBins(dataF) > > # Normalize binned read counts to have diploid normal copy number > dataN <- normalizeBins(dataC) > > # Segment copy numbers > set.seed(42) ## segmentBins() relies on RNG via DNAcopy::segment() > fit <- segmentBins(dataN) > > # Call copy-number segments > fitC <- callBins(fit) There were 50 or more warnings (use warnings() to see the first 50) > > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # REPRODUCIBILITY > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > strategies <- c("sequential", "multisession") > if (parallelly::supportsMulticore()) strategies <- c(strategies, "multicore") > > oplan <- future::plan("list") > for (strategy in strategies) { + message(sprintf("Reproducibility with plan(\"%s\") ...", strategy)) + + future::plan(strategy) + + dataFr <- applyFilters(data, residual=TRUE, blacklist=TRUE) + stopifnot(all.equal(dataFr, dataF)) + + dataCr <- correctBins(dataF) + stopifnot(all.equal(dataCr, dataC)) + + dataNr <- normalizeBins(dataC) + stopifnot(all.equal(dataNr, dataN)) + + set.seed(42) ## segmentBins() relies on RNG via DNAcopy::segment() + fitr <- segmentBins(dataNr) + stopifnot(all.equal(fitr, fit)) + + fitCr <- callBins(fitr) + stopifnot(all.equal(fitCr, fitC)) + + message(sprintf("Reproducibility with plan(\"%s\") ... done", strategy)) + } Reproducibility with plan("sequential") ... Reproducibility with plan("sequential") ... done Reproducibility with plan("multisession") ... Calculating fit for sample LGG150 (1 of 1) ... Segmenting: LGG150 (1 of 1) ... Reproducibility with plan("multisession") ... done Reproducibility with plan("multicore") ... Reproducibility with plan("multicore") ... done There were 50 or more warnings (use warnings() to see the first 50) > > future::plan(oplan) > > proc.time() user system elapsed 60.147 1.434 79.377
QDNAseq.Rcheck/tests/QDNAseq.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(QDNAseq) > library(Biobase) ## combine(), sampleNames() Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > library(utils) > > do_plot <- TRUE > do_cleanup <- TRUE > > # Load data > data(LGG150) > data <- LGG150 > print(data) QDNAseqReadCounts (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: counts protocolData: none phenoData sampleNames: LGG150 varLabels: name reads used.reads expected.variance varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > stopifnot(inherits(data, "QDNAseqReadCounts")) > > # Plot isobars of read counts > if (do_plot) isobarPlot(data) Plotting sample LGG150 median read counts > > # Plot copy number profile > if (do_plot) { + plot(data, ylim=c(-100, 200)) + highlightFilters(data, residual=TRUE, blacklist=TRUE) + } Plotting sample LGG150 (1 of 1) ... Highlighted 3,375 bins. > > # Filter out "bad" bins > dataF <- applyFilters(data, residual=TRUE, blacklist=TRUE) 38,819 total bins 38,819 of which in selected chromosomes 36,722 of which with reference sequence 33,347 final bins > print(dataF) QDNAseqReadCounts (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: counts protocolData: none phenoData sampleNames: LGG150 varLabels: name reads used.reads expected.variance varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > if (do_plot) plot(dataF, ylim=c(-100, 200)) Plotting sample LGG150 (1 of 1) ... > stopifnot(inherits(dataF, "QDNAseqReadCounts")) > > # Correct read counts as a function of GC content and mappability > dataC <- correctBins(dataF) Calculating correction for GC content and mappability Calculating fit for sample LGG150 (1 of 1) ... Done. > print(dataC) QDNAseqCopyNumbers (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: copynumber protocolData: none phenoData sampleNames: LGG150 varLabels: name reads ... loess.family (6 total) varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > if (do_plot) plot(dataC, ylim=c(-100, 200)) Plotting sample LGG150 (1 of 1) ... > stopifnot(inherits(dataC, "QDNAseqCopyNumbers")) > > # Normalize binned read counts to have diploid normal copy number > dataN <- normalizeBins(dataC) Applying median normalization ... > print(dataN) QDNAseqCopyNumbers (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: copynumber protocolData: none phenoData sampleNames: LGG150 varLabels: name reads ... loess.family (6 total) varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > if (do_plot) plot(dataN) Plotting sample LGG150 (1 of 1) ... > stopifnot(inherits(dataN, "QDNAseqCopyNumbers")) > > # Plot noise > if (do_plot) noisePlot(dataF) Calculating correction for GC content and mappability Calculating fit for sample LGG150 (1 of 1) ... Done. > > # Segment copy numbers > fit <- segmentBins(dataN) Performing segmentation: Segmenting: LGG150 (1 of 1) ... > print(fit) QDNAseqCopyNumbers (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: copynumber, segmented protocolData: none phenoData sampleNames: LGG150 varLabels: name reads ... loess.family (6 total) varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > if (do_plot) plot(fit) Plotting sample LGG150 (1 of 1) ... > stopifnot(inherits(fit, "QDNAseqCopyNumbers")) > > # Call copy-number segments > fitC <- callBins(fit) EM algorithm started ... [1] "Total number of segments present in the data: 10" [1] "Number of segments used for fitting the model: 9" 39112268039979208.961.4770358214954667411.5114.1770358212395555411.594.6 Calling iteration1: optim results time: 0 minimum: 16445.6418287481 116443.1634295677-0.939948404909664-0.5351158716347120.04999922851584940.1357341814220170.2320391157632851.492692224927890.46336036623653-0.0007447487965535120.0111894143724591-0.000962583906213420.3145629342085070.798554843389167 3912731804343020961.4770358214954667411.5114.1770358212395555411.594.6 Calling iteration2: optim results time: 0 minimum: 16445.5781374328 116443.1331012469-0.932876677515083-0.535943303880990.0499979048415910.1114729434735370.1905642555481931.861013902305770.4314700360573740.0001440687684080910.01118427659401560.0007568920162792620.2061088124299370.874022351578009 3912730804342920961.4770358214954667411.5114.1770358212395555411.594.6 Calling iteration3: optim results time: 0 minimum: 16445.5975371627 116443.1273697069-0.924012853099601-0.5365177469718870.04999923288882760.108573194240180.1856071014916831.753751992204390.4694950401327692.93313204145295e-050.0111878614439676-0.0001759851682342870.07360543573369820.943675664015282 EM algorithm done ... Computing posterior probabilities for all segments ... Total time:0minutes Adjusting segmented data for cellularity ... Cellularity sample1: 1 Adjusting normalized data for cellularity ... Cellularity sample1: 1 1 39153998264664209.263.1770358214954667411.5114.1770358212395555411.594.6 39154188431410209.264.4770358214954667411.5114.1770358212395555411.594.6 39154158431404209.264.4770358214954667411.5114.1770358212395555411.594.6 39154438698419209.266.4770358214954667411.5114.1770358212395555411.594.6 39158608699353209.266.4770358214954667411.5114.1770358212395555411.594.6 39158698699357209.266.4770358214954667411.5114.1770358212395555411.594.6 39158788699361209.266.4770358214954667411.5114.1770358212395555411.594.6 39158878699365209.266.4770358214954667411.5114.1770358212395555411.594.6 39158968699369209.266.4770358214954667411.5114.1770358212395555411.594.6 39159028699372209.266.4770358214954667411.5114.1770358212395555411.594.6 39159218766102209.266.9770358214954667411.5114.1770358212395555411.594.6 39163388766482209.266.9770358214954667411.5114.1770358212395555411.594.6 FINISHED! Total time:0minutes There were 50 or more warnings (use warnings() to see the first 50) > print(fitC) QDNAseqCopyNumbers (storageMode: lockedEnvironment) assayData: 38819 features, 1 samples element names: calls, copynumber, probamp, probdloss, probgain, probloss, probnorm, segmented protocolData: none phenoData sampleNames: LGG150 varLabels: name reads ... loess.family (6 total) varMetadata: labelDescription featureData featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747 (38819 total) fvarLabels: chromosome start ... use (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > if (do_plot) plot(fitC) Plotting sample LGG150 (1 of 1) ... > > > # --------------------------------------------------------------- > # Exporting > # --------------------------------------------------------------- > message("* exportBins() ...") * exportBins() ... > > sets <- list(data = data, dataC = dataC, fit = fit, fitC = fitC) > for (name in names(sets)) { + set <- sets[[name]] + formats <- c("tsv", "igv", "bed") + if (name == "fitC") formats <- c(formats, "vcf", "seg") + for (format in formats) { + types <- c("copynumber") + if (name %in% c("fit", "fitC")) types <- c(types, "segments") + if (name == "fitC") types <- c(types, "calls") + for (type in types) { + fileext <- sprintf(".%s.%s", type, format) + templates <- c("QDNAseq-%s.", "QDNAseq-%i.", "QDNAseq-%03i.") + if (ncol(set) == 1L || !(format %in% c("bed", "seg", "vcf"))) { + templates <- c("QDNAseq.", templates) + } + for (template in templates) { + file <- tempfile(pattern = template, fileext = fileext) + message(sprintf(" - exportBins(<%d samples>, format=\"%s\", type=\"%s\", file=\"%s\")", ncol(set), format, type, template)) + file <- exportBins(set, file = file, format = format, type = type) + message(sprintf(" File(s) written: [n=%d] %s", + length(file), paste(sQuote(file), collapse = ", "))) + stopifnot(all(file_test("-f", file))) + if (do_cleanup) { + file.remove(file) + stopifnot(!any(file_test("-f", file))) + } + } + } + } + } - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825494686d516.copynumber.tsv' - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.1825492cdcdfb3.copynumber.tsv' - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.1825495be89fa0.copynumber.tsv' - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.182549499a03e1.copynumber.tsv' - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.18254912fd2153.copynumber.igv' - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.18254930dbf85e.copynumber.igv' - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.18254920f1d328.copynumber.igv' - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.18254945bdc58f.copynumber.igv' - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.182549c793277.copynumber.bed' - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-LGG150.18254930fa5e71.copynumber.bed' - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-1.18254969be2555.copynumber.bed' - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-001.182549473c12d8.copynumber.bed' - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825491885c37e.copynumber.tsv' - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.1825493d3c2999.copynumber.tsv' - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.18254910e214e.copynumber.tsv' - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.182549403a77d1.copynumber.tsv' - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.18254958682f31.copynumber.igv' - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.18254929a2c483.copynumber.igv' - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.1825497df1f08c.copynumber.igv' - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.1825494c8114dc.copynumber.igv' - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.182549277900e0.copynumber.bed' - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-LGG150.18254961e3b424.copynumber.bed' - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-1.182549121e99ad.copynumber.bed' - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-001.1825497cdc2aac.copynumber.bed' - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825496d21e7f9.copynumber.tsv' - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.1825495516f034.copynumber.tsv' - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.1825491d9847e1.copynumber.tsv' - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.1825494037158e.copynumber.tsv' - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825491d2a1cec.segments.tsv' - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.18254977cbc784.segments.tsv' - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.18254952c04316.segments.tsv' - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.18254963b0f202.segments.tsv' - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.18254924a8a737.copynumber.igv' - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.1825492ea8e2b6.copynumber.igv' - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.1825492d4af5e3.copynumber.igv' - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.18254937a5c88b.copynumber.igv' - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825495f84db14.segments.igv' - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.1825494e3cc90b.segments.igv' - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.1825497d638e1a.segments.igv' - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.1825496bfe0d8b.segments.igv' - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825497f37277c.copynumber.bed' - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-LGG150.1825496721b36f.copynumber.bed' - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-1.182549333a2063.copynumber.bed' - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-001.18254917bceafa.copynumber.bed' - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.182549245ddd09.segments.bed' - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-LGG150.182549344841b1.segments.bed' - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-1.18254957f762cc.segments.bed' - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-001.1825497cc60c3a.segments.bed' - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825495deb0634.copynumber.tsv' - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.18254955e95358.copynumber.tsv' - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.18254949472117.copynumber.tsv' - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.1825495640714.copynumber.tsv' - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.18254937cd077c.segments.tsv' - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.1825495b65bac4.segments.tsv' - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.18254924031c0.segments.tsv' - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.18254924eeef75.segments.tsv' - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.182549307caaf9.calls.tsv' - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.1825491fd879a1.calls.tsv' - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.18254965260503.calls.tsv' - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.1825494da6c7e5.calls.tsv' - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.18254917a44125.copynumber.igv' - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.18254937e64819.copynumber.igv' - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.1825493157b9e7.copynumber.igv' - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.1825493c4ce85d.copynumber.igv' - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.182549668f2acf.segments.igv' - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.1825495ea2afca.segments.igv' - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.18254973f2b0e8.segments.igv' - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.182549461405e3.segments.igv' - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825492cdf78d6.calls.igv' - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.18254971563f02.calls.igv' - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.1825493212136e.calls.igv' - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.1825492c16a052.calls.igv' - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825495877f271.copynumber.bed' - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-LGG150.182549654c33d1.copynumber.bed' - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-1.18254943d38b4d.copynumber.bed' - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-001.1825497cd5cf7a.copynumber.bed' - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.18254919947582.segments.bed' - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-LGG150.1825491bcaee19.segments.bed' - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-1.182549799bdbb5.segments.bed' - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-001.182549777f7bb6.segments.bed' - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.18254971b44171.calls.bed' - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-LGG150.18254942e2fccc.calls.bed' - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-1.1825497ce382ca.calls.bed' - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-001.182549298148ed.calls.bed' - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825491e48b790.copynumber.vcf' - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-LGG150.1825497f23b48b.copynumber.vcf' - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-1.1825494e703862.copynumber.vcf' - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-001.1825494ec56289.copynumber.vcf' - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825491efc2e2c.segments.vcf' - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-LGG150.18254933963d65.segments.vcf' - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-1.1825491c6c2a6e.segments.vcf' - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-001.18254936a06f52.segments.vcf' - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825496b7c857e.calls.vcf' - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-LGG150.1825494dc3e455.calls.vcf' - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-1.18254972ed57af.calls.vcf' - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-001.182549520bb04d.calls.vcf' - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825492c669420.copynumber.seg' - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-LGG150.18254966e00897.copynumber.seg' - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-1.182549181fb630.copynumber.seg' - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-001.18254959460cf6.copynumber.seg' - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.18254958364799.segments.seg' - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-LGG150.1825494a31c99e.segments.seg' - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-1.18254955cad48.segments.seg' - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-001.18254930ae3a0a.segments.seg' - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825492f7dfd6f.calls.seg' - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-LGG150.18254949303895.calls.seg' - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-1.1825492d840985.calls.seg' - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-001.182549491272f1.calls.seg' > > sets <- list(data = data, dataC = dataC, fit = fit, fitC = fitC) > sets <- lapply(sets, FUN = function(set) { + stopifnot(ncol(set) == 1L) + name <- sampleNames(set) + setA <- set + sampleNames(setA) <- sprintf("%sa", name) + setB <- set + sampleNames(setB) <- sprintf("%sb", name) + combine(setA, setB) + }) > > for (name in names(sets)) { + set <- sets[[name]] + stopifnot(ncol(set) == 2L) + formats <- c("tsv", "igv", "bed") + if (name == "fitC") formats <- c(formats, "vcf", "seg") + for (format in formats) { + types <- c("copynumber") + if (name %in% c("fit", "fitC")) types <- c(types, "segments") + if (name == "fitC") types <- c(types, "calls") + for (type in types) { + fileext <- sprintf(".%s.%s", type, format) + templates <- c("QDNAseq-%s.", "QDNAseq-%i.", "QDNAseq-%03i.") + if (ncol(set) == 1L || !(format %in% c("bed", "seg", "vcf"))) { + templates <- c("QDNAseq.", templates) + } + for (template in templates) { + file <- tempfile(pattern = template, fileext = fileext) + message(sprintf(" - exportBins(<%d samples>, format=\"%s\", type=\"%s\", file=\"%s\")", ncol(set), format, type, template)) + file <- exportBins(set, file = file, format = format, type = type) + message(sprintf(" File(s) written: [n=%d] %s", + length(file), paste(sQuote(file), collapse = ", "))) + stopifnot(all(file_test("-f", file))) + if (do_cleanup) { + file.remove(file) + stopifnot(!any(file_test("-f", file))) + } + } + } + } + } - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.18254964fb26ae.copynumber.tsv' - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.182549271fe53a.copynumber.tsv' - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.1825494091eea7.copynumber.tsv' - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.18254956af681f.copynumber.tsv' - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825496a02e206.copynumber.igv' - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.1825493d757171.copynumber.igv' - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.18254930b10c.copynumber.igv' - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.18254984b9996.copynumber.igv' - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-LGG150a.1825493c9925fc.copynumber.bed', '/tmp/RtmpPnhbUV/QDNAseq-LGG150b.1825493c9925fc.copynumber.bed' - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-1.1825494ea0e96e.copynumber.bed', '/tmp/RtmpPnhbUV/QDNAseq-2.1825494ea0e96e.copynumber.bed' - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-001.1825495710fc20.copynumber.bed', '/tmp/RtmpPnhbUV/QDNAseq-002.1825495710fc20.copynumber.bed' - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825495b955429.copynumber.tsv' - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.18254923726d3.copynumber.tsv' - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.182549737d268e.copynumber.tsv' - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.1825491235c37b.copynumber.tsv' - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825496db3ac51.copynumber.igv' - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.18254941410ae4.copynumber.igv' - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.1825495231b2a.copynumber.igv' - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.1825493fbf5c9e.copynumber.igv' - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-LGG150a.1825496da79f04.copynumber.bed', '/tmp/RtmpPnhbUV/QDNAseq-LGG150b.1825496da79f04.copynumber.bed' - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-1.1825496c0323c1.copynumber.bed', '/tmp/RtmpPnhbUV/QDNAseq-2.1825496c0323c1.copynumber.bed' - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-001.18254957df12ce.copynumber.bed', '/tmp/RtmpPnhbUV/QDNAseq-002.18254957df12ce.copynumber.bed' - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.18254946edabfa.copynumber.tsv' - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.18254944396b5a.copynumber.tsv' - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.1825492210dc6c.copynumber.tsv' - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.1825494c4a5942.copynumber.tsv' - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.18254974e7a564.segments.tsv' - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.182549518ed9db.segments.tsv' - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.182549157a91d8.segments.tsv' - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.182549226baee9.segments.tsv' - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825491aa14ccc.copynumber.igv' - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.1825497a75b886.copynumber.igv' - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.182549498b9423.copynumber.igv' - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.1825495b333b73.copynumber.igv' - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.182549512520a6.segments.igv' - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.182549338e7629.segments.igv' - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.18254918a8ace5.segments.igv' - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.1825495155d1b2.segments.igv' - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-LGG150a.1825493bda0fc0.copynumber.bed', '/tmp/RtmpPnhbUV/QDNAseq-LGG150b.1825493bda0fc0.copynumber.bed' - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-1.1825495541d2e1.copynumber.bed', '/tmp/RtmpPnhbUV/QDNAseq-2.1825495541d2e1.copynumber.bed' - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-001.1825491ff6bb21.copynumber.bed', '/tmp/RtmpPnhbUV/QDNAseq-002.1825491ff6bb21.copynumber.bed' - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%s.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-LGG150a.18254912eb0be0.segments.bed', '/tmp/RtmpPnhbUV/QDNAseq-LGG150b.18254912eb0be0.segments.bed' - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-1.18254930d7270a.segments.bed', '/tmp/RtmpPnhbUV/QDNAseq-2.18254930d7270a.segments.bed' - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%03i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-001.182549222de1f4.segments.bed', '/tmp/RtmpPnhbUV/QDNAseq-002.182549222de1f4.segments.bed' - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.182549668326e.copynumber.tsv' - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.182549430cea85.copynumber.tsv' - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.182549fe18e46.copynumber.tsv' - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.18254947a93d52.copynumber.tsv' - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.182549483005af.segments.tsv' - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.1825494fa0eae4.segments.tsv' - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.1825493550dc56.segments.tsv' - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.18254934332970.segments.tsv' - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.182549277ffdb3.calls.tsv' - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.1825497c3e8850.calls.tsv' - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.182549786c94ca.calls.tsv' - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.1825494990da1f.calls.tsv' - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.1825494888e193.copynumber.igv' - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.1825496d543a2f.copynumber.igv' - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.1825491b1fb3fb.copynumber.igv' - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.1825495e03736b.copynumber.igv' - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.182549fbfe918.segments.igv' - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.18254935c100c7.segments.igv' - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.18254958792bf1.segments.igv' - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.182549594b7d3c.segments.igv' - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq.18254910f43c3b.calls.igv' - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%s.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%s.182549299e4c97.calls.igv' - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%i.182549cd9f365.calls.igv' - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%03i.") File(s) written: [n=1] '/tmp/RtmpPnhbUV/QDNAseq-%03i.182549299ce920.calls.igv' - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-LGG150a.1825497af41e4a.copynumber.bed', '/tmp/RtmpPnhbUV/QDNAseq-LGG150b.1825497af41e4a.copynumber.bed' - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-1.18254948b40325.copynumber.bed', '/tmp/RtmpPnhbUV/QDNAseq-2.18254948b40325.copynumber.bed' - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-001.1825497edebc01.copynumber.bed', '/tmp/RtmpPnhbUV/QDNAseq-002.1825497edebc01.copynumber.bed' - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%s.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-LGG150a.1825491aead96b.segments.bed', '/tmp/RtmpPnhbUV/QDNAseq-LGG150b.1825491aead96b.segments.bed' - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-1.1825495b9f0f05.segments.bed', '/tmp/RtmpPnhbUV/QDNAseq-2.1825495b9f0f05.segments.bed' - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%03i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-001.1825492fb5e30c.segments.bed', '/tmp/RtmpPnhbUV/QDNAseq-002.1825492fb5e30c.segments.bed' - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%s.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-LGG150a.1825493d18bb5f.calls.bed', '/tmp/RtmpPnhbUV/QDNAseq-LGG150b.1825493d18bb5f.calls.bed' - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-1.18254962074174.calls.bed', '/tmp/RtmpPnhbUV/QDNAseq-2.18254962074174.calls.bed' - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%03i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-001.18254972c2cd91.calls.bed', '/tmp/RtmpPnhbUV/QDNAseq-002.18254972c2cd91.calls.bed' - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-LGG150a.1825494cfa49a5.copynumber.vcf', '/tmp/RtmpPnhbUV/QDNAseq-LGG150b.1825494cfa49a5.copynumber.vcf' - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-1.18254929b07ec6.copynumber.vcf', '/tmp/RtmpPnhbUV/QDNAseq-2.18254929b07ec6.copynumber.vcf' - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-001.1825493af2d341.copynumber.vcf', '/tmp/RtmpPnhbUV/QDNAseq-002.1825493af2d341.copynumber.vcf' - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%s.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-LGG150a.1825491c9b348a.segments.vcf', '/tmp/RtmpPnhbUV/QDNAseq-LGG150b.1825491c9b348a.segments.vcf' - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-1.1825495f015b1d.segments.vcf', '/tmp/RtmpPnhbUV/QDNAseq-2.1825495f015b1d.segments.vcf' - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%03i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-001.1825496f25fcb1.segments.vcf', '/tmp/RtmpPnhbUV/QDNAseq-002.1825496f25fcb1.segments.vcf' - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%s.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-LGG150a.182549441b323d.calls.vcf', '/tmp/RtmpPnhbUV/QDNAseq-LGG150b.182549441b323d.calls.vcf' - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-1.1825495b3fe36d.calls.vcf', '/tmp/RtmpPnhbUV/QDNAseq-2.1825495b3fe36d.calls.vcf' - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%03i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-001.1825496792917c.calls.vcf', '/tmp/RtmpPnhbUV/QDNAseq-002.1825496792917c.calls.vcf' - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%s.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-LGG150a.182549dac0c5c.copynumber.seg', '/tmp/RtmpPnhbUV/QDNAseq-LGG150b.182549dac0c5c.copynumber.seg' - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-1.18254923c8c500.copynumber.seg', '/tmp/RtmpPnhbUV/QDNAseq-2.18254923c8c500.copynumber.seg' - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%03i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-001.18254954e6cbab.copynumber.seg', '/tmp/RtmpPnhbUV/QDNAseq-002.18254954e6cbab.copynumber.seg' - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%s.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-LGG150a.18254928cbc057.segments.seg', '/tmp/RtmpPnhbUV/QDNAseq-LGG150b.18254928cbc057.segments.seg' - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-1.1825491cc386b.segments.seg', '/tmp/RtmpPnhbUV/QDNAseq-2.1825491cc386b.segments.seg' - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%03i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-001.18254964a6b4c3.segments.seg', '/tmp/RtmpPnhbUV/QDNAseq-002.18254964a6b4c3.segments.seg' - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%s.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-LGG150a.1825495e8cc11f.calls.seg', '/tmp/RtmpPnhbUV/QDNAseq-LGG150b.1825495e8cc11f.calls.seg' - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-1.1825495a45645d.calls.seg', '/tmp/RtmpPnhbUV/QDNAseq-2.1825495a45645d.calls.seg' - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%03i.") File(s) written: [n=2] '/tmp/RtmpPnhbUV/QDNAseq-001.1825493df231ff.calls.seg', '/tmp/RtmpPnhbUV/QDNAseq-002.1825493df231ff.calls.seg' > > message("* exportBins() ... done") * exportBins() ... done > > proc.time() user system elapsed 45.176 1.180 49.552
QDNAseq.Rcheck/QDNAseq-Ex.timings
name | user | system | elapsed | |
addPhenodata | 0.075 | 0.006 | 0.081 | |
applyFilters | 0.234 | 0.008 | 0.245 | |
binReadCounts | 0 | 0 | 0 | |
callBins | 16.398 | 0.148 | 19.075 | |
compareToReference | 1.311 | 0.026 | 2.112 | |
correctBins | 1.198 | 0.007 | 2.145 | |
createBins | 0 | 0 | 0 | |
estimateCorrection | 1.134 | 0.005 | 1.171 | |
exportBins | 0 | 0 | 0 | |
frequencyPlot | 15.709 | 0.012 | 18.006 | |
getBinAnnotations | 0 | 0 | 0 | |
highlightFilters | 0.387 | 0.013 | 0.406 | |
isobarPlot | 0.761 | 0.013 | 0.781 | |
makeCgh | 1.255 | 0.005 | 1.777 | |
noisePlot | 1.207 | 0.002 | 1.452 | |
normalizeBins | 1.171 | 0.003 | 1.214 | |
normalizeSegmentedBins | 5.286 | 0.004 | 6.446 | |
plot | 1.891 | 0.027 | 2.221 | |
poolRuns | 0.084 | 0.003 | 0.087 | |
segmentBins | 5.180 | 0.007 | 6.576 | |
smoothOutlierBins | 1.232 | 0.007 | 1.248 | |