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This page was generated on 2024-05-27 11:35:30 -0400 (Mon, 27 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4752
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4517
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 1641/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QDNAseq 1.40.0  (landing page)
Daoud Sie
Snapshot Date: 2024-05-26 14:00:09 -0400 (Sun, 26 May 2024)
git_url: https://git.bioconductor.org/packages/QDNAseq
git_branch: RELEASE_3_19
git_last_commit: 44d22b7
git_last_commit_date: 2024-04-30 10:35:34 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for QDNAseq on nebbiolo1


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.

raw results


Summary

Package: QDNAseq
Version: 1.40.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:QDNAseq.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings QDNAseq_1.40.0.tar.gz
StartedAt: 2024-05-27 02:01:50 -0400 (Mon, 27 May 2024)
EndedAt: 2024-05-27 02:08:43 -0400 (Mon, 27 May 2024)
EllapsedTime: 412.8 seconds
RetCode: 0
Status:   OK  
CheckDir: QDNAseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:QDNAseq.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings QDNAseq_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/QDNAseq.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘QDNAseq/DESCRIPTION’ ... OK
* this is package ‘QDNAseq’ version ‘1.40.0’
* 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 ... NOTE
checkRd: (-1) exportBins.Rd:41: Lost braces
    41 |         \code{"bed"}.  This argument is ignored if code{type = "calls"}.}
       |                                                        ^
* 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
frequencyPlot          19.843  0.024  19.867
callBins               18.712  0.616  19.328
segmentBins             7.160  0.003   7.164
normalizeSegmentedBins  6.979  0.008   6.987
* 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’
 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/QDNAseq.Rcheck/00check.log’
for details.


Installation output

QDNAseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL QDNAseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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)

Tests output

QDNAseq.Rcheck/tests/binReadCounts.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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 v1.34.0
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] "/home/biocbuild/bbs-3.19-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 
  6.212   0.224   6.427 

QDNAseq.Rcheck/tests/QDNAseq,copyneutral.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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, 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"
38855308006595207.661.1768507515027574410.5114.7768507510313594410.578.7
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
38870358010016207.661.2768507515027574410.5114.7768507510313594410.578.7
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
38897038231770207.862.9768507515027574410.5114.7768507510748146410.582.1
38897228398516207.864.1768507515027574410.5114.7768507510748146410.582.1
38897198398510207.864.1768507515027574410.5114.7768507510748146410.582.1
38897478665290207.866.2768507515027574410.5114.7768507510748146410.582.1
38901648666224207.866.2768507515027574410.5114.7768507510748146410.582.1
38901738666228207.866.2768507515027574410.5114.7768507510748146410.582.1
38901828666232207.866.2768507515027574410.5114.7768507510748146410.582.1
38901918666236207.866.2768507515027574410.5114.7768507510748146410.582.1
38902008666240207.866.2768507515027574410.5114.7768507510748146410.582.1
38902068666243207.866.2768507515027574410.5114.7768507510748146410.582.1
38902258732973207.866.7768507515027574410.5114.7768507510748146410.582.1
38906428733353207.866.7768507515027574410.5114.7768507510748146410.582.1
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/RtmpfcSYTv/QDNAseq-%seb3e0278268ef.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments")
    File(s) written: [n=1] '/tmp/RtmpfcSYTv/QDNAseq-%seb3e05655da77.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls")
    File(s) written: [n=1] '/tmp/RtmpfcSYTv/QDNAseq-%seb3e0369726b4.calls.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmpfcSYTv/QDNAseq-%seb3e03b834485.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments")
    File(s) written: [n=1] '/tmp/RtmpfcSYTv/QDNAseq-%seb3e0460f4341.segments.igv'
  - exportBins(<1 samples>, format="igv", type="calls")
    File(s) written: [n=1] '/tmp/RtmpfcSYTv/QDNAseq-%seb3e0c25eb38.calls.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmpfcSYTv/QDNAseq-LGG150eb3e04e64a0cb.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments")
    File(s) written: [n=1] '/tmp/RtmpfcSYTv/QDNAseq-LGG150eb3e01e5a64ba.segments.bed'
  - exportBins(<1 samples>, format="bed", type="calls")
    File(s) written: [n=1] '/tmp/RtmpfcSYTv/QDNAseq-LGG150eb3e072497a2c.calls.bed'
  - exportBins(<1 samples>, format="seg", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmpfcSYTv/QDNAseq-LGG150eb3e090b51c8.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/RtmpfcSYTv/QDNAseq-LGG150eb3e0316e2457.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/RtmpfcSYTv/QDNAseq-LGG150eb3e02f97e1d9.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/RtmpfcSYTv/QDNAseq-LGG150eb3e01711dbe5.copynumber.vcf'
character(0)
  - exportBins(<1 samples>, format="vcf", type="segments")
    File(s) written: [n=1] '/tmp/RtmpfcSYTv/QDNAseq-LGG150eb3e073669f4f.segments.vcf'
character(0)
  - exportBins(<1 samples>, format="vcf", type="calls")
    File(s) written: [n=1] '/tmp/RtmpfcSYTv/QDNAseq-LGG150eb3e026838d53.calls.vcf'
character(0)
> 
> proc.time()
   user  system elapsed 
 21.085   0.794  21.869 

QDNAseq.Rcheck/tests/QDNAseq,gain-copyneutral-gain.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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, 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"
38858408050174207.661.5768507515027574410.5114.7768507510313483410.578.7
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
38900138275157207.863.2768507515027574410.5114.7768507510791852410.582.4
38900328441903207.864.5768507515027574410.5114.7768507510791852410.582.4
38900298441897207.864.5768507515027574410.5114.7768507510791852410.582.4
38900578710427207.866.5768507515027574410.5114.7768507510791852410.582.4
38904748711361207.866.5768507515027574410.5114.7768507510791852410.582.4
38904838711365207.866.5768507515027574410.5114.7768507510791852410.582.4
38904928711369207.866.5768507515027574410.5114.7768507510791852410.582.4
38905018711373207.866.5768507515027574410.5114.7768507510791852410.582.4
38905108711377207.866.5768507515027574410.5114.7768507510791852410.582.4
38905168711380207.866.5768507515027574410.5114.7768507510791852410.582.4
38905358778110207.867768507515027574410.5114.7768507510791852410.582.4
38909528778490207.867768507515027574410.5114.7768507510791852410.582.4
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/RtmpFqFMJh/QDNAseq-%sebb9b72ccdff6.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments")
    File(s) written: [n=1] '/tmp/RtmpFqFMJh/QDNAseq-%sebb9b38435b5b.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls")
    File(s) written: [n=1] '/tmp/RtmpFqFMJh/QDNAseq-%sebb9b5d77446b.calls.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmpFqFMJh/QDNAseq-%sebb9b70992586.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments")
    File(s) written: [n=1] '/tmp/RtmpFqFMJh/QDNAseq-%sebb9ba17a49e.segments.igv'
  - exportBins(<1 samples>, format="igv", type="calls")
    File(s) written: [n=1] '/tmp/RtmpFqFMJh/QDNAseq-%sebb9b3cea9638.calls.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmpFqFMJh/QDNAseq-LGG150ebb9b7ea561be.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments")
    File(s) written: [n=1] '/tmp/RtmpFqFMJh/QDNAseq-LGG150ebb9b55e4786d.segments.bed'
  - exportBins(<1 samples>, format="bed", type="calls")
    File(s) written: [n=1] '/tmp/RtmpFqFMJh/QDNAseq-LGG150ebb9b68e8734a.calls.bed'
  - exportBins(<1 samples>, format="seg", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmpFqFMJh/QDNAseq-LGG150ebb9b22a55516.copynumber.seg'
                                                 SAMPLE_NAME CHROMOSOME
1 /tmp/RtmpFqFMJh/QDNAseq-LGG150ebb9b22a55516.copynumber.seg          7
2 /tmp/RtmpFqFMJh/QDNAseq-LGG150ebb9b22a55516.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/RtmpFqFMJh/QDNAseq-LGG150ebb9b6f5d73e9.segments.seg'
                                               SAMPLE_NAME CHROMOSOME    START
1 /tmp/RtmpFqFMJh/QDNAseq-LGG150ebb9b6f5d73e9.segments.seg          7 37110001
2 /tmp/RtmpFqFMJh/QDNAseq-LGG150ebb9b6f5d73e9.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/RtmpFqFMJh/QDNAseq-LGG150ebb9b6433daef.calls.seg'
                                            SAMPLE_NAME CHROMOSOME    START
1 /tmp/RtmpFqFMJh/QDNAseq-LGG150ebb9b6433daef.calls.seg          7 37110001
2 /tmp/RtmpFqFMJh/QDNAseq-LGG150ebb9b6433daef.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/RtmpFqFMJh/QDNAseq-LGG150ebb9b2ded1174.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/RtmpFqFMJh/QDNAseq-LGG150ebb9b62f03fe3.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/RtmpFqFMJh/QDNAseq-LGG150ebb9b6440f01b.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 
 18.860   0.497  19.347 

QDNAseq.Rcheck/tests/QDNAseq,parallel-reproducibility.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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 
 69.810   1.725  80.716 

QDNAseq.Rcheck/tests/QDNAseq.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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, 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)
> 
> # 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
> isobarPlot(data)
Plotting sample LGG150 median read counts
> 
> # Plot copy number profile
> plot(data, ylim=c(-100, 200))
Plotting sample LGG150 (1 of 1) ...
> highlightFilters(data, residual=TRUE, blacklist=TRUE)
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:  
> 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:  
> 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:  
> plot(dataN)
Plotting sample LGG150 (1 of 1) ...
> stopifnot(inherits(dataN, "QDNAseqCopyNumbers"))
> 
> # Plot noise
> 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:  
> 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"
38999318013488208.361.2768382415058718410.4114.9768382412482265410.495.3
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
39014368016939208.461.2768382415058718410.4114.9768382412482265410.495.3
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
39014358016938208.461.2768382415058718410.4114.9768382412482265410.495.3
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
39041048238173208.662.9768382415058718410.4114.9768382412482265410.495.3
39041238404919208.664.2768382415058718410.4114.9768382412482265410.495.3
39041208404913208.664.2768382415058718410.4114.9768382412482265410.495.3
39041488671928208.666.2768382415058718410.4114.9768382412482265410.495.3
39045658672862208.666.2768382415058718410.4114.9768382412482265410.495.3
39045748672866208.666.2768382415058718410.4114.9768382412482265410.495.3
39045838672870208.666.2768382415058718410.4114.9768382412482265410.495.3
39045928672874208.666.2768382415058718410.4114.9768382412482265410.495.3
39046018672878208.666.2768382415058718410.4114.9768382412482265410.495.3
39046078672881208.666.2768382415058718410.4114.9768382412482265410.495.3
39046268739611208.666.7768382415058718410.4114.9768382412482265410.495.3
39050438739991208.666.7768382415058718410.4114.9768382412482265410.495.3
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:  
> 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)))
+         file.remove(file)
+         stopifnot(!any(file_test("-f", file)))
+       }
+     }
+   }
+ }
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f045345704224.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f04537329a023.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f04534bedc485.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f04531c38dca2.copynumber.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f04535e0d13d9.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f0453773013f2.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f0453307d0604.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f0453b8f13c.copynumber.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f04531bca4932.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-LGG150.f045374658fe1.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-1.f0453d3d2eec.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-001.f04536234ab1.copynumber.bed'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f045375308da0.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f045342631b16.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f04532d075a42.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f045349166d5.copynumber.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f04532d5baf7f.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f045358c7c970.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f045351d28a48.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f04534345bdfd.copynumber.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f0453116901cb.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-LGG150.f04536b552175.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-1.f04534144cce4.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-001.f04537c544c5d.copynumber.bed'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f0453117ace9f.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f04535ecab7f8.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f0453eb07287.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f045332fde1.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f045323359f1.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f04534644b848.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f045377047ec9.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f045347a39c15.segments.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f0453396e586c.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f045342f2434f.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f045363dc78b7.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f0453177b6c45.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f04533a225741.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f045314597ebb.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f045318345d82.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f045355eca073.segments.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f04538bf0e9d.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-LGG150.f045325718c6e.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-1.f04535c0feb24.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-001.f04537def9c3d.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f045367d4a784.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-LGG150.f04539174567.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-1.f04532810312.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-001.f045315305703.segments.bed'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f045361df0ed7.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f045354538d5b.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f045358761501.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f0453734810a2.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f04533fa8aed0.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f045319bae1e5.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f04536f9c5cff.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f045351237d6f.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f0453788599dd.calls.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f04537e4ccf86.calls.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f045351567b50.calls.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f04537ab8f3cf.calls.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f0453449187cf.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f0453485afa19.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f0453425c8fe4.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f04537dffe03b.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f0453b4d3d68.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f04532639089c.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f0453157b4c80.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f0453456f94aa.segments.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f04533a928757.calls.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f04532dafaa02.calls.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f04531b5c351d.calls.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f0453435195f4.calls.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f045353213671.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-LGG150.f0453776c2042.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-1.f045341413231.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-001.f04533af5ddf5.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f04538365a9.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-LGG150.f045343c23544.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-1.f0453502634f9.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-001.f045362627480.segments.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f04531815c29f.calls.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-LGG150.f0453289c49fa.calls.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-1.f045355aa8522.calls.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-001.f045357be716f.calls.bed'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f045342572bdf.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-LGG150.f04534546e222.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-1.f045328e1eede.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-001.f04533adcc5bc.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f04534393b1a8.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-LGG150.f04537a386a2e.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-1.f04533595b98b.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-001.f04538253977.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f045342936447.calls.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-LGG150.f045377f24970.calls.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-1.f045362519b2.calls.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-001.f04534de0a1b0.calls.vcf'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f04531e2b520c.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-LGG150.f04531ba06633.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-1.f04531350365a.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-001.f045358bdd963.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f045349501035.segments.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-LGG150.f04532eac6b77.segments.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-1.f04531c0f6f58.segments.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-001.f04531c7146a6.segments.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f045326188bb9.calls.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-LGG150.f04535d50a189.calls.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-1.f04535767249c.calls.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-001.f0453269bf162.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)))
+         file.remove(file)
+         stopifnot(!any(file_test("-f", file)))
+       }
+     }
+   }
+ }
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f04532112d6cd.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f0453278d5995.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f04538fe65e2.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f04533928996c.copynumber.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f04535029a38f.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f04535ea8eb05.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f045310e70adb.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f04531280cf6e.copynumber.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-LGG150a.f045323efcd27.copynumber.bed', '/tmp/RtmpprvBiB/QDNAseq-LGG150b.f045323efcd27.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-1.f045339c8f9b9.copynumber.bed', '/tmp/RtmpprvBiB/QDNAseq-2.f045339c8f9b9.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-001.f04534d5d952a.copynumber.bed', '/tmp/RtmpprvBiB/QDNAseq-002.f04534d5d952a.copynumber.bed'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f045367837ecf.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f0453340163e7.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f04532f34eb6.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f04536fa8b847.copynumber.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f04537694c82f.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f04537ae59826.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f045375cdd1f9.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f0453447569df.copynumber.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-LGG150a.f04531910ea32.copynumber.bed', '/tmp/RtmpprvBiB/QDNAseq-LGG150b.f04531910ea32.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-1.f0453116e382c.copynumber.bed', '/tmp/RtmpprvBiB/QDNAseq-2.f0453116e382c.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-001.f045357c5a039.copynumber.bed', '/tmp/RtmpprvBiB/QDNAseq-002.f045357c5a039.copynumber.bed'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f045371cec395.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f04535abe4862.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f04536720bb0.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f0453dde32ed.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f0453772f8f08.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f04532c8a976a.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f04536b2ed477.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f04534e96b3a4.segments.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f0453532688cc.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f0453c41ab44.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f045376240d39.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f04535c24eeaf.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f0453456a44b1.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f0453464db0c8.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f04533acdd9b4.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f045356514f8c.segments.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-LGG150a.f045358ce8036.copynumber.bed', '/tmp/RtmpprvBiB/QDNAseq-LGG150b.f045358ce8036.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-1.f04535ebda6db.copynumber.bed', '/tmp/RtmpprvBiB/QDNAseq-2.f04535ebda6db.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-001.f0453101a4946.copynumber.bed', '/tmp/RtmpprvBiB/QDNAseq-002.f0453101a4946.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-LGG150a.f0453262c1561.segments.bed', '/tmp/RtmpprvBiB/QDNAseq-LGG150b.f0453262c1561.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-1.f0453464125aa.segments.bed', '/tmp/RtmpprvBiB/QDNAseq-2.f0453464125aa.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-001.f0453441bad2d.segments.bed', '/tmp/RtmpprvBiB/QDNAseq-002.f0453441bad2d.segments.bed'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f0453291f6417.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f045335e9ddf1.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f04533ab0755c.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f04532404fc3d.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f04532bb7afeb.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f04537f25df3b.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f04533d15e66f.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f04533d25e817.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f045356eb7f74.calls.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f04532ee4aa04.calls.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f045317e43079.calls.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f04535d5d8b25.calls.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f04533cc2dcf2.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f0453f13bf82.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f04539e8228f.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f045327f1b169.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f04535daa7326.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f04535d0eab5b.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f045334335cad.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f045353ce8060.segments.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq.f045339339a0a.calls.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%s.f0453799da15e.calls.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%i.f04531a1c3128.calls.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpprvBiB/QDNAseq-%03i.f0453740173be.calls.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-LGG150a.f04534feef0eb.copynumber.bed', '/tmp/RtmpprvBiB/QDNAseq-LGG150b.f04534feef0eb.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-1.f045372eab15f.copynumber.bed', '/tmp/RtmpprvBiB/QDNAseq-2.f045372eab15f.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-001.f045352bf1a99.copynumber.bed', '/tmp/RtmpprvBiB/QDNAseq-002.f045352bf1a99.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-LGG150a.f045360093a31.segments.bed', '/tmp/RtmpprvBiB/QDNAseq-LGG150b.f045360093a31.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-1.f04531916c6c0.segments.bed', '/tmp/RtmpprvBiB/QDNAseq-2.f04531916c6c0.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-001.f045319004044.segments.bed', '/tmp/RtmpprvBiB/QDNAseq-002.f045319004044.segments.bed'
  - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-LGG150a.f04532424e75e.calls.bed', '/tmp/RtmpprvBiB/QDNAseq-LGG150b.f04532424e75e.calls.bed'
  - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-1.f045342362ad7.calls.bed', '/tmp/RtmpprvBiB/QDNAseq-2.f045342362ad7.calls.bed'
  - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-001.f04534eea1e35.calls.bed', '/tmp/RtmpprvBiB/QDNAseq-002.f04534eea1e35.calls.bed'
  - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-LGG150a.f04535ed55cbb.copynumber.vcf', '/tmp/RtmpprvBiB/QDNAseq-LGG150b.f04535ed55cbb.copynumber.vcf'
  - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-1.f0453663b2714.copynumber.vcf', '/tmp/RtmpprvBiB/QDNAseq-2.f0453663b2714.copynumber.vcf'
  - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-001.f04537aa1ce20.copynumber.vcf', '/tmp/RtmpprvBiB/QDNAseq-002.f04537aa1ce20.copynumber.vcf'
  - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-LGG150a.f04535dfb3bf6.segments.vcf', '/tmp/RtmpprvBiB/QDNAseq-LGG150b.f04535dfb3bf6.segments.vcf'
  - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-1.f045323510d83.segments.vcf', '/tmp/RtmpprvBiB/QDNAseq-2.f045323510d83.segments.vcf'
  - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-001.f045337c7b638.segments.vcf', '/tmp/RtmpprvBiB/QDNAseq-002.f045337c7b638.segments.vcf'
  - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-LGG150a.f045334e6bb6b.calls.vcf', '/tmp/RtmpprvBiB/QDNAseq-LGG150b.f045334e6bb6b.calls.vcf'
  - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-1.f04535235b787.calls.vcf', '/tmp/RtmpprvBiB/QDNAseq-2.f04535235b787.calls.vcf'
  - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-001.f04534fabe6b1.calls.vcf', '/tmp/RtmpprvBiB/QDNAseq-002.f04534fabe6b1.calls.vcf'
  - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-LGG150a.f045312444690.copynumber.seg', '/tmp/RtmpprvBiB/QDNAseq-LGG150b.f045312444690.copynumber.seg'
  - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-1.f0453ef89479.copynumber.seg', '/tmp/RtmpprvBiB/QDNAseq-2.f0453ef89479.copynumber.seg'
  - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-001.f04535ebfa633.copynumber.seg', '/tmp/RtmpprvBiB/QDNAseq-002.f04535ebfa633.copynumber.seg'
  - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-LGG150a.f04531c2c691f.segments.seg', '/tmp/RtmpprvBiB/QDNAseq-LGG150b.f04531c2c691f.segments.seg'
  - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-1.f045336ea45e2.segments.seg', '/tmp/RtmpprvBiB/QDNAseq-2.f045336ea45e2.segments.seg'
  - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-001.f04533c6a195a.segments.seg', '/tmp/RtmpprvBiB/QDNAseq-002.f04533c6a195a.segments.seg'
  - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-LGG150a.f0453793b147a.calls.seg', '/tmp/RtmpprvBiB/QDNAseq-LGG150b.f0453793b147a.calls.seg'
  - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-1.f04536b1da290.calls.seg', '/tmp/RtmpprvBiB/QDNAseq-2.f04536b1da290.calls.seg'
  - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpprvBiB/QDNAseq-001.f0453103899ba.calls.seg', '/tmp/RtmpprvBiB/QDNAseq-002.f0453103899ba.calls.seg'
> 
> message("* exportBins() ... done")
* exportBins() ... done
> 
> proc.time()
   user  system elapsed 
 70.396   0.928  71.317 

Example timings

QDNAseq.Rcheck/QDNAseq-Ex.timings

nameusersystemelapsed
addPhenodata0.1150.0040.119
applyFilters0.2840.0080.291
binReadCounts0.0000.0000.001
callBins18.712 0.61619.328
compareToReference1.9620.1482.110
correctBins1.7480.0001.748
createBins000
estimateCorrection1.7040.0001.703
exportBins0.0010.0000.000
frequencyPlot19.843 0.02419.867
getBinAnnotations000
highlightFilters0.7980.0280.826
isobarPlot1.0020.0161.018
makeCgh1.8720.0001.872
noisePlot1.7750.0041.779
normalizeBins1.8050.0041.809
normalizeSegmentedBins6.9790.0086.987
plot2.4870.0082.495
poolRuns0.1250.0040.130
segmentBins7.1600.0037.164
smoothOutlierBins1.7940.0041.797