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This page was generated on 2021-12-03 13:05:59 -0500 (Fri, 03 Dec 2021).

CHECK results for QDNAseq on machv2

To the developers/maintainers of the QDNAseq package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1496/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QDNAseq 1.30.0  (landing page)
Daoud Sie
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/QDNAseq
git_branch: RELEASE_3_14
git_last_commit: cd4ceaa
git_last_commit_date: 2021-10-27 16:34:47 -0500 (Wed, 27 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: QDNAseq
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:QDNAseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings QDNAseq_1.30.0.tar.gz
StartedAt: 2021-12-02 18:08:14 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 18:16:41 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 507.1 seconds
RetCode: 0
Status:   OK  
CheckDir: QDNAseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:QDNAseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings QDNAseq_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/QDNAseq.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QDNAseq/DESCRIPTION’ ... OK
* this is package ‘QDNAseq’ version ‘1.30.0’
* 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 R 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
callBins               21.881  0.336  22.233
frequencyPlot          20.019  0.168  20.208
normalizeSegmentedBins  8.283  0.060   8.350
segmentBins             8.049  0.033   8.087
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

QDNAseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL QDNAseq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 v1.24.0
QDNAseq bin annotations for Hsapiens, build hg19.
Created by Ilari Scheinin with QDNAseq 0.7.5, 2014-02-06 09:20:46.
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] "/Library/Frameworks/R.framework/Versions/4.1/Resources/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 
  8.755   0.442   9.192 

QDNAseq.Rcheck/tests/QDNAseq,copyneutral.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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, 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, sort, 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"
39415488021668210.661.3789275715780588421.6120.4NA65536789275710836499421.682.7
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
39430538025089210.661.3789275715780588421.6120.4NA65536789275710836499421.682.7
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
39457218246843210.863789275715780588421.6120.4NA65536789275710836499421.682.7
39457408413589210.864.2789275715780588421.6120.4NA65536789275710836499421.682.7
39457378413583210.864.2789275715780588421.6120.4NA65536789275710836499421.682.7
39457658680363210.866.3789275715780588421.6120.4NA65536789275710836499421.682.7
39461928681318210.866.3789275715780588421.6120.4NA65536789275710836499421.682.7
39462018681322210.866.3789275715780588421.6120.4NA65536789275710836499421.682.7
39462108681326210.866.3789275715780588421.6120.4NA65536789275710836499421.682.7
39462198681330210.866.3789275715780588421.6120.4NA65536789275710836499421.682.7
39462288681334210.866.3789275715780588421.6120.4NA65536789275710836499421.682.7
39462348681337210.866.3789275715780588421.6120.4NA65536789275710836499421.682.7
39462538748067210.866.8789275715780588421.6120.4NA65536789275710836499421.682.7
39466708748390210.866.8789275715780588421.6120.4NA65536789275710836499421.682.7
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/Rtmp9PvGy3/QDNAseq-%s15c53c9e8afa.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments")
    File(s) written: [n=1] '/tmp/Rtmp9PvGy3/QDNAseq-%s15c537cb6298e.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls")
    File(s) written: [n=1] '/tmp/Rtmp9PvGy3/QDNAseq-%s15c531b626999.calls.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber")
    File(s) written: [n=1] '/tmp/Rtmp9PvGy3/QDNAseq-%s15c535a02c9da.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments")
    File(s) written: [n=1] '/tmp/Rtmp9PvGy3/QDNAseq-%s15c536d123560.segments.igv'
  - exportBins(<1 samples>, format="igv", type="calls")
    File(s) written: [n=1] '/tmp/Rtmp9PvGy3/QDNAseq-%s15c53466e6991.calls.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber")
    File(s) written: [n=1] '/tmp/Rtmp9PvGy3/QDNAseq-LGG15015c537ad4d2b6.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments")
    File(s) written: [n=1] '/tmp/Rtmp9PvGy3/QDNAseq-LGG15015c532a55e9ba.segments.bed'
  - exportBins(<1 samples>, format="bed", type="calls")
    File(s) written: [n=1] '/tmp/Rtmp9PvGy3/QDNAseq-LGG15015c536e63c80c.calls.bed'
  - exportBins(<1 samples>, format="seg", type="copynumber")
    File(s) written: [n=1] '/tmp/Rtmp9PvGy3/QDNAseq-LGG15015c5358e2c472.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/Rtmp9PvGy3/QDNAseq-LGG15015c53fcf45f5.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/Rtmp9PvGy3/QDNAseq-LGG15015c5370f9dfee.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/Rtmp9PvGy3/QDNAseq-LGG15015c5324dcbc34.copynumber.vcf'
character(0)
  - exportBins(<1 samples>, format="vcf", type="segments")
    File(s) written: [n=1] '/tmp/Rtmp9PvGy3/QDNAseq-LGG15015c5317c80cd4.segments.vcf'
character(0)
  - exportBins(<1 samples>, format="vcf", type="calls")
    File(s) written: [n=1] '/tmp/Rtmp9PvGy3/QDNAseq-LGG15015c534ec23e7e.calls.vcf'
character(0)
> 
> proc.time()
   user  system elapsed 
 24.258   0.800  25.064 

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


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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, 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, sort, 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"
39418588065247210.661.6789275715780588421.6120.4NA65536789275710836065421.682.7
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
39460318290230210.863.3789275715780588421.6120.4NA65536789275710836065421.682.7
39460508456976210.864.6789275715780588421.6120.4NA65536789275710836065421.682.7
39460478456970210.864.6789275715780588421.6120.4NA65536789275710836065421.682.7
39460758725500210.866.6789275715780588421.6120.4NA65536789275710836065421.682.7
39465028726455210.866.6789275715780588421.6120.4NA65536789275710836065421.682.7
39465118726459210.866.6789275715780588421.6120.4NA65536789275710836065421.682.7
39465208726463210.866.6789275715780588421.6120.4NA65536789275710836065421.682.7
39465298726467210.866.6789275715780588421.6120.4NA65536789275710836065421.682.7
39465388726471210.866.6789275715780588421.6120.4NA65536789275710836065421.682.7
39465448726474210.866.6789275715780588421.6120.4NA65536789275710836065421.682.7
39465638793204210.867.1789275715780588421.6120.4NA65536789275710836065421.682.7
39469808793527210.867.1789275715780588421.6120.4NA65536789275710836065421.682.7
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/RtmpzDki8f/QDNAseq-%s16076c99fd7b.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments")
    File(s) written: [n=1] '/tmp/RtmpzDki8f/QDNAseq-%s1607651d09cb3.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls")
    File(s) written: [n=1] '/tmp/RtmpzDki8f/QDNAseq-%s1607656dfd5bb.calls.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmpzDki8f/QDNAseq-%s16076149148c.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments")
    File(s) written: [n=1] '/tmp/RtmpzDki8f/QDNAseq-%s1607664e3f3fc.segments.igv'
  - exportBins(<1 samples>, format="igv", type="calls")
    File(s) written: [n=1] '/tmp/RtmpzDki8f/QDNAseq-%s1607631a75923.calls.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmpzDki8f/QDNAseq-LGG1501607661cd224c.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments")
    File(s) written: [n=1] '/tmp/RtmpzDki8f/QDNAseq-LGG150160766286ddbd.segments.bed'
  - exportBins(<1 samples>, format="bed", type="calls")
    File(s) written: [n=1] '/tmp/RtmpzDki8f/QDNAseq-LGG15016076447d5d4.calls.bed'
  - exportBins(<1 samples>, format="seg", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmpzDki8f/QDNAseq-LGG15016076827537e.copynumber.seg'
                                                SAMPLE_NAME CHROMOSOME    START
1 /tmp/RtmpzDki8f/QDNAseq-LGG15016076827537e.copynumber.seg          7 37110001
2 /tmp/RtmpzDki8f/QDNAseq-LGG15016076827537e.copynumber.seg          7 90165001
       STOP DATAPOINTS LOG2_RATIO_MEAN
1  68955000       1487            0.99
2 122010000       2012            0.99
  - exportBins(<1 samples>, format="seg", type="segments")
    File(s) written: [n=1] '/tmp/RtmpzDki8f/QDNAseq-LGG150160764dda7960.segments.seg'
                                               SAMPLE_NAME CHROMOSOME    START
1 /tmp/RtmpzDki8f/QDNAseq-LGG150160764dda7960.segments.seg          7 37110001
2 /tmp/RtmpzDki8f/QDNAseq-LGG150160764dda7960.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/RtmpzDki8f/QDNAseq-LGG150160764256b58e.calls.seg'
                                            SAMPLE_NAME CHROMOSOME    START
1 /tmp/RtmpzDki8f/QDNAseq-LGG150160764256b58e.calls.seg          7 37110001
2 /tmp/RtmpzDki8f/QDNAseq-LGG150160764256b58e.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/RtmpzDki8f/QDNAseq-LGG150160764aa99fa8.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/RtmpzDki8f/QDNAseq-LGG150160764630f4e3.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/RtmpzDki8f/QDNAseq-LGG15016076381d8715.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 
 24.525   0.752  25.337 

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


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 
 78.885   1.618  91.437 

QDNAseq.Rcheck/tests/QDNAseq.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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, 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, sort, 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"
39550708026359211.361.3770335115275770411.5116.6NA65536770335112663142411.596.7
Calling iteration1:

optim results
time: 1
minimum: 16445.6418287481
116443.1634295677-0.939948404909672-0.5351158716347190.04999922851584940.1357341814220170.2320391157632851.492692224927890.46336036623653-0.000744748796554230.0111894143724591-0.000962583906213420.3145629342085070.798554843389167
39565758029810211.461.3770335115275770411.5116.6NA65536770335112663142411.596.7
Calling iteration2:

optim results
time: 0
minimum: 16445.5781374328
116443.1331012469-0.932876677515091-0.5359433038809970.0499979048415910.1114729434735370.1905642555481931.861013902305770.4314700360573740.0001440687684073730.01118427659401560.0007568920162792620.2061088124299370.874022351578009
39565758029810211.461.3770335115275770411.5116.6NA65536770335112663142411.596.7
Calling iteration3:

optim results
time: 0
minimum: 16445.5975371627
116443.1273697069-0.924012853099608-0.5365177469718940.04999923288882760.108573194240180.1856071014916831.753751992204390.4694950401327692.93313204138107e-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
39592438251044211.563770335115275770411.5116.6NA65536770335112663142411.596.7
39592628417790211.564.3770335115275770411.5116.6NA65536770335112663142411.596.7
39592598417784211.564.3770335115275770411.5116.6NA65536770335112663142411.596.7
39592878684799211.566.3770335115275770411.5116.6NA65536770335112663142411.596.7
39597148685754211.566.3770335115275770411.5116.6NA65536770335112663142411.596.7
39597238685758211.566.3770335115275770411.5116.6NA65536770335112663142411.596.7
39597328685762211.566.3770335115275770411.5116.6NA65536770335112663142411.596.7
39597418685766211.566.3770335115275770411.5116.6NA65536770335112663142411.596.7
39597508685770211.566.3770335115275770411.5116.6NA65536770335112663142411.596.7
39597568685773211.566.3770335115275770411.5116.6NA65536770335112663142411.596.7
39597758752503211.566.8770335115275770411.5116.6NA65536770335112663142411.596.7
39601928752826211.566.8770335115275770411.5116.6NA65536770335112663142411.596.7
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/RtmpkgxnYE/QDNAseq.179286a226e65.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.179287a7ddf52.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.179285dd0bf51.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.1792833c08ef5.copynumber.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.1792826e9915e.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.179283046c647.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.1792876837813.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.179283140642e.copynumber.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179287a712144.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-LGG150.17928193f3629.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-1.179284fccab2.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-001.17928705f6eac.copynumber.bed'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.1792895b17d7.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.179283b7a290d.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.17928511d32fc.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.1792853fe67fe.copynumber.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.17928635d7fc6.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.17928f6fd321.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.17928768e2371.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.179286db90c85.copynumber.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.17928fe5280a.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-LGG150.17928da7b0ad.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-1.179287c4034db.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-001.179285b4e5597.copynumber.bed'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.1792873d55b55.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.179283c5f64dc.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.179281ad6c67b.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.17928a80c301.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.17928b827c0a.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.17928239d7a6d.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.1792837d09c5f.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.1792860ca3d99.segments.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179287d923973.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.17928af9ed6d.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.179281e5294bc.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.179283fa2d231.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179285a95af9a.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.17928193bd5ec.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.17928275985e5.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.1792866659191.segments.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179281637fb1c.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-LGG150.179283546f6a9.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-1.1792845ebec92.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-001.179283f8891b.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.1792831f14da6.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-LGG150.179285920e6e7.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-1.179287f177567.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-001.179285d1cfe60.segments.bed'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179281a808062.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.179286a6caf85.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.179285777b59.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.17928674312dc.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.17928648b5e7a.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.1792879e7cf27.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.1792861d147f7.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.1792872cbdb4c.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.1792825aa9575.calls.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.17928623a47a4.calls.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.179286035925d.calls.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.179285d1c4903.calls.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179286bfd93b6.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.1792854ecc91d.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.17928587ba7a.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.1792811e3a26c.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.1792877bc69a0.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.1792872bac4c9.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.1792843cda2f7.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.17928718628e7.segments.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179281ee78feb.calls.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.1792874999d26.calls.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.17928111c6598.calls.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.179285f51e6ee.calls.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179287a104425.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-LGG150.1792841ea17be.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-1.179286fbcdcc0.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-001.179285840fa8f.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179281201ef8d.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-LGG150.179283d161b37.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-1.179287654d735.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-001.179283bfd1544.segments.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.17928647f4220.calls.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-LGG150.179285ece766b.calls.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-1.1792844c09b6d.calls.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-001.17928411c345e.calls.bed'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.1792822b228b7.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-LGG150.179285e8f182c.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-1.1792847c2134.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-001.179287167df38.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179285a700fb2.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-LGG150.1792873169d80.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-1.1792851be7987.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-001.17928301cb7fe.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179282d739d5f.calls.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-LGG150.17928160df49.calls.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-1.179287ee33253.calls.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-001.1792875fd2839.calls.vcf'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179283f5bf2b3.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-LGG150.179282d9ae644.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-1.17928148391c0.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-001.1792849d5dec5.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.1792878147d61.segments.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-LGG150.17928933a8de.segments.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-1.179281e938b8a.segments.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-001.1792868ae20b4.segments.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179287fe53f1c.calls.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-LGG150.17928239288dd.calls.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-1.1792869577769.calls.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-001.179286d60c486.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/RtmpkgxnYE/QDNAseq.179286c067183.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.179281b0686dd.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.1792849802507.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.179287bff1443.copynumber.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.17928278b7a4e.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.17928360aab2a.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.17928766b6e1d.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.1792870a6ea8.copynumber.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-LGG150a.179283de6db34.copynumber.bed', '/tmp/RtmpkgxnYE/QDNAseq-LGG150b.179283de6db34.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-1.179287f4152ab.copynumber.bed', '/tmp/RtmpkgxnYE/QDNAseq-2.179287f4152ab.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-001.17928199a99d2.copynumber.bed', '/tmp/RtmpkgxnYE/QDNAseq-002.17928199a99d2.copynumber.bed'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.1792874e8b71f.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.179285a4e902f.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.179285bdc2bfa.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.1792853cb5933.copynumber.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179284b4d4e3f.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.17928404c30b8.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.179284a12a102.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.17928d08b04c.copynumber.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-LGG150a.17928356e5443.copynumber.bed', '/tmp/RtmpkgxnYE/QDNAseq-LGG150b.17928356e5443.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-1.179285e5e161c.copynumber.bed', '/tmp/RtmpkgxnYE/QDNAseq-2.179285e5e161c.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-001.1792872fdb8aa.copynumber.bed', '/tmp/RtmpkgxnYE/QDNAseq-002.1792872fdb8aa.copynumber.bed'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179286f66dbe0.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.1792849ed8843.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.1792898d0ca0.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.17928b37e146.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179281a6c06b.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.179286aa2b1a5.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.179285f3cfe54.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.179281d5d6da5.segments.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.1792860c97ab2.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.179284b966dc2.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.179281000253.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.17928279897a8.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.17928130caae7.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.1792824a82d76.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.179281d40b0c7.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.17928215e7d2.segments.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-LGG150a.179286c268d0f.copynumber.bed', '/tmp/RtmpkgxnYE/QDNAseq-LGG150b.179286c268d0f.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-1.1792856f70b41.copynumber.bed', '/tmp/RtmpkgxnYE/QDNAseq-2.1792856f70b41.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-001.1792875040501.copynumber.bed', '/tmp/RtmpkgxnYE/QDNAseq-002.1792875040501.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-LGG150a.179285ae4c0ab.segments.bed', '/tmp/RtmpkgxnYE/QDNAseq-LGG150b.179285ae4c0ab.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-1.179286025492b.segments.bed', '/tmp/RtmpkgxnYE/QDNAseq-2.179286025492b.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-001.179282fe6d75d.segments.bed', '/tmp/RtmpkgxnYE/QDNAseq-002.179282fe6d75d.segments.bed'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179285c45333c.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.179284326d777.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.179282b0be812.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.179281ab10bd2.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.179285d7f15ae.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.1792842688276.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.179285b4d3309.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.179282951c2b3.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.1792836c58af6.calls.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.1792863263891.calls.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.17928624bea71.calls.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.17928660cd321.calls.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.1792853f94fde.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.1792814eaa2e4.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.17928386c3176.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.17928472356ea.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.17928611f4122.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.179284aed50fe.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.1792822607a20.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.179286bf1dc81.segments.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq.1792853c3d084.calls.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%s.179285caeb512.calls.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%i.1792851f1e047.calls.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmpkgxnYE/QDNAseq-%03i.179285ebb7f58.calls.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-LGG150a.1792867a59afe.copynumber.bed', '/tmp/RtmpkgxnYE/QDNAseq-LGG150b.1792867a59afe.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-1.179282962cedb.copynumber.bed', '/tmp/RtmpkgxnYE/QDNAseq-2.179282962cedb.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-001.1792815faa117.copynumber.bed', '/tmp/RtmpkgxnYE/QDNAseq-002.1792815faa117.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-LGG150a.179287965f846.segments.bed', '/tmp/RtmpkgxnYE/QDNAseq-LGG150b.179287965f846.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-1.17928158ef9ee.segments.bed', '/tmp/RtmpkgxnYE/QDNAseq-2.17928158ef9ee.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-001.179285dba8350.segments.bed', '/tmp/RtmpkgxnYE/QDNAseq-002.179285dba8350.segments.bed'
  - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-LGG150a.1792832943.calls.bed', '/tmp/RtmpkgxnYE/QDNAseq-LGG150b.1792832943.calls.bed'
  - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-1.179284f89edb6.calls.bed', '/tmp/RtmpkgxnYE/QDNAseq-2.179284f89edb6.calls.bed'
  - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-001.1792868557085.calls.bed', '/tmp/RtmpkgxnYE/QDNAseq-002.1792868557085.calls.bed'
  - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-LGG150a.17928414e6146.copynumber.vcf', '/tmp/RtmpkgxnYE/QDNAseq-LGG150b.17928414e6146.copynumber.vcf'
  - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-1.17928d45c29.copynumber.vcf', '/tmp/RtmpkgxnYE/QDNAseq-2.17928d45c29.copynumber.vcf'
  - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-001.1792875ee882b.copynumber.vcf', '/tmp/RtmpkgxnYE/QDNAseq-002.1792875ee882b.copynumber.vcf'
  - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-LGG150a.179287f2dfb89.segments.vcf', '/tmp/RtmpkgxnYE/QDNAseq-LGG150b.179287f2dfb89.segments.vcf'
  - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-1.1792823dd209a.segments.vcf', '/tmp/RtmpkgxnYE/QDNAseq-2.1792823dd209a.segments.vcf'
  - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-001.17928a8770db.segments.vcf', '/tmp/RtmpkgxnYE/QDNAseq-002.17928a8770db.segments.vcf'
  - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-LGG150a.1792842023f43.calls.vcf', '/tmp/RtmpkgxnYE/QDNAseq-LGG150b.1792842023f43.calls.vcf'
  - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-1.1792821876990.calls.vcf', '/tmp/RtmpkgxnYE/QDNAseq-2.1792821876990.calls.vcf'
  - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-001.1792841237e22.calls.vcf', '/tmp/RtmpkgxnYE/QDNAseq-002.1792841237e22.calls.vcf'
  - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-LGG150a.1792812e0b97.copynumber.seg', '/tmp/RtmpkgxnYE/QDNAseq-LGG150b.1792812e0b97.copynumber.seg'
  - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-1.1792875fae71b.copynumber.seg', '/tmp/RtmpkgxnYE/QDNAseq-2.1792875fae71b.copynumber.seg'
  - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-001.179282b5ada20.copynumber.seg', '/tmp/RtmpkgxnYE/QDNAseq-002.179282b5ada20.copynumber.seg'
  - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-LGG150a.1792859a6811c.segments.seg', '/tmp/RtmpkgxnYE/QDNAseq-LGG150b.1792859a6811c.segments.seg'
  - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-1.179284266833f.segments.seg', '/tmp/RtmpkgxnYE/QDNAseq-2.179284266833f.segments.seg'
  - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-001.179285832bf27.segments.seg', '/tmp/RtmpkgxnYE/QDNAseq-002.179285832bf27.segments.seg'
  - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-LGG150a.179286ba3c6ad.calls.seg', '/tmp/RtmpkgxnYE/QDNAseq-LGG150b.179286ba3c6ad.calls.seg'
  - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-1.179284d48bf10.calls.seg', '/tmp/RtmpkgxnYE/QDNAseq-2.179284d48bf10.calls.seg'
  - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmpkgxnYE/QDNAseq-001.1792862f7db13.calls.seg', '/tmp/RtmpkgxnYE/QDNAseq-002.1792862f7db13.calls.seg'
> 
> message("* exportBins() ... done")
* exportBins() ... done
> 
> proc.time()
   user  system elapsed 
 87.269   4.421  92.039 

Example timings

QDNAseq.Rcheck/QDNAseq-Ex.timings

nameusersystemelapsed
addPhenodata0.2310.0110.241
applyFilters0.3470.0100.355
binReadCounts0.0000.0010.000
callBins21.881 0.33622.233
compareToReference3.7350.0803.818
correctBins2.8890.0162.907
createBins0.0000.0000.001
estimateCorrection3.0840.0143.100
exportBins0.0000.0010.001
frequencyPlot20.019 0.16820.208
getBinAnnotations000
highlightFilters0.7140.0740.790
isobarPlot1.6040.0271.634
makeCgh3.1560.0403.196
noisePlot2.8480.0142.863
normalizeBins3.4490.0243.475
normalizeSegmentedBins8.2830.0608.350
plot3.9070.0673.978
poolRuns0.1940.0020.196
segmentBins8.0490.0338.087
smoothOutlierBins2.9800.0253.006