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This page was generated on 2021-10-21 12:05:00 -0400 (Thu, 21 Oct 2021).

CHECK results for QDNAseq on riesling1

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 1491/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QDNAseq 1.29.5  (landing page)
Daoud Sie
Snapshot Date: 2021-10-20 14:50:05 -0400 (Wed, 20 Oct 2021)
git_url: https://git.bioconductor.org/packages/QDNAseq
git_branch: master
git_last_commit: a32bf44
git_last_commit_date: 2021-10-20 13:07:57 -0400 (Wed, 20 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  YES
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  YES
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: QDNAseq
Version: 1.29.5
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QDNAseq.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings QDNAseq_1.29.5.tar.gz
StartedAt: 2021-10-21 03:23:55 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 03:34:51 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 655.9 seconds
RetCode: 0
Status:   OK  
CheckDir: QDNAseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QDNAseq.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings QDNAseq_1.29.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/QDNAseq.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'QDNAseq/DESCRIPTION' ... OK
* this is package 'QDNAseq' version '1.29.5'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
frequencyPlot          17.79   0.02   17.81
callBins               17.23   0.06   17.30
normalizeSegmentedBins 10.06   0.01   10.08
segmentBins            10.00   0.00   10.00
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
callBins               13.89   0.11   14.00
frequencyPlot          13.82   0.01   13.83
segmentBins             5.70   0.03    5.73
normalizeSegmentedBins  5.58   0.03    5.61
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'QDNAseq,copyneutral.R'
  Running 'QDNAseq,gain-copyneutral-gain.R'
  Running 'QDNAseq,parallel-reproducibility.R'
  Running 'QDNAseq.R'
  Running 'binReadCounts.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/QDNAseq_1.29.5.tar.gz && rm -rf QDNAseq.buildbin-libdir && mkdir QDNAseq.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=QDNAseq.buildbin-libdir QDNAseq_1.29.5.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL QDNAseq_1.29.5.zip && rm QDNAseq_1.29.5.tar.gz QDNAseq_1.29.5.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:03 --:--:--     0
100  585k  100  585k    0     0   161k      0  0:00:03  0:00:03 --:--:--  161k
100  585k  100  585k    0     0   161k      0  0:00:03  0:00:03 --:--:--  161k

install for i386

* installing *source* package 'QDNAseq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'QDNAseq'
    finding HTML links ... done
    LGG150                                  html  
    QDNAseq-defunct                         html  
    QDNAseq-package                         html  
    QDNAseqCopyNumbers                      html  
    QDNAseqReadCounts                       html  
    QDNAseqSignals                          html  
    addPhenodata                            html  
    applyFilters                            html  
    binReadCounts                           html  
    callBins                                html  
    compareToReference                      html  
    correctBins                             html  
    createBins                              html  
    estimateCorrection                      html  
    exportBins                              html  
    finding level-2 HTML links ... done

    frequencyPlot                           html  
    getBinAnnotations                       html  
    highlightFilters                        html  
    isobarPlot                              html  
    makeCgh                                 html  
    noisePlot                               html  
    normalizeBins                           html  
    normalizeSegmentedBins                  html  
    plot                                    html  
    poolRuns                                html  
    segmentBins                             html  
    smoothOutlierBins                       html  
** 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

install for x64

* installing *source* package 'QDNAseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QDNAseq' as QDNAseq_1.29.5.zip
* DONE (QDNAseq)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'QDNAseq' successfully unpacked and MD5 sums checked

Tests output

QDNAseq.Rcheck/tests_i386/binReadCounts.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 v1.23.0
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] "D:/biocbuild/bbs-3.14-bioc/R/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 
   4.03    0.20    4.23 

QDNAseq.Rcheck/tests_x64/binReadCounts.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 v1.23.0
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] "D:/biocbuild/bbs-3.14-bioc/R/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 
   4.21    0.21    4.43 

QDNAseq.Rcheck/tests_i386/QDNAseq.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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"
39042525522246119.242.2801664212255594244.793.6801664210146329244.777.5
Calling iteration1:

optim results
time: 0
minimum: 16445.6418287481
116443.1634295677-0.939948404909672-0.5351158716347190.04999922851584940.1357341814220170.2320391157632851.492692224927890.46336036623653-0.000744748796554230.0111894143724591-0.000962583906213420.3145629342085070.798554843389167
39057575524593119.242.2801664212255594244.793.6801664210146329244.777.5
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
39057575524593119.242.2801664212255594244.793.6801664210146329244.777.5
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
39084255727422119.343.7801664212255594244.793.6801664210146329244.777.5
39084445894166119.345801664212255594244.793.6801664210146329244.777.5
39084415894162119.345801664212255594244.793.6801664210146329244.777.5
39084696161177119.347.1801664212255594244.793.6801664210146329244.777.5
39088966161815119.347.1801664212255594244.793.6801664210146329244.777.5
39089056161818119.347.1801664212255594244.793.6801664210146329244.777.5
39089146161821119.347.1801664212255594244.793.6801664210146329244.777.5
39089236161824119.347.1801664212255594244.793.6801664210146329244.777.5
39089326161827119.347.1801664212255594244.793.6801664210146329244.777.5
39089386161829119.347.1801664212255594244.793.6801664210146329244.777.5
39089576228543119.347.6801664212255594244.793.6801664210146329244.777.5
39093746228780119.447.6801664212255594244.793.6801664210146329244.777.5
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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac101c3c1aff.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac10711c191d.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac1067324be4.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac103817568e.copynumber.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac105e0d6a52.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac10573576ca.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac1073c862bb.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac10ee537f4.copynumber.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac104ee74363.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150.ac1031697290.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac1085b4215.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac1078da6cda.copynumber.bed'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac1051a64a15.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac107e6c785c.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac10463f2655.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac1036f3dbf.copynumber.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac106c381beb.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac1018a65ae2.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac10281e8c3.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac104e237729.copynumber.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac1028215a91.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150.ac101ab43218.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac10a74720a.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac1053d13020.copynumber.bed'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac1042f74654.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac1013e649b8.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac104145cbb.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac10a5660b0.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac102ee668a5.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac10cbf1fc2.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac10ea127c8.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac104d80586b.segments.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac10632e4e9a.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac105b7872f9.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac107f151909.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac104f1124e4.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac107ca0536d.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac10487d6161.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac104e3e6fbb.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac1023403835.segments.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac102e257afb.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150.ac102ef16c7.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac10313b6fc.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac101d371f7a.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac101375c46.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150.ac106520b39.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac10203850.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac107b934954.segments.bed'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac1066651bf3.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac1091b518a.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac1077df2e1f.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac1064e85c67.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac1015d476cd.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac102d1975d0.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac102feb1634.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac10343b1ddc.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac103fb95c40.calls.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac10680c6be5.calls.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac1059a2440.calls.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac10158567df.calls.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac10cdf18df.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac102e18de9.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac103b2f7455.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac1072373022.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac106f2710de.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac1025152abe.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac1072445d6b.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac102db01e59.segments.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac104203a98.calls.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac10490f248a.calls.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac1074463df.calls.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac1031c832bc.calls.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac103afa90b.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150.ac1060c61f39.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac104af77bef.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac104b497c88.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac102a273657.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150.ac10422e3ef9.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac1028eb7c3f.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac105671607e.segments.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac10aba5e43.calls.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150.ac1066f076bc.calls.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac10220c2057.calls.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac103b726f62.calls.bed'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac10637678b8.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150.ac1050e766ba.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac1034163b23.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac103af24c7e.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac1077314444.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150.ac103ea44aec.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac101f1b3971.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac10a8b241c.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac1045577098.calls.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150.ac102feb7992.calls.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac10e001476.calls.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac10414b3210.calls.vcf'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac105a67590a.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150.ac103a3371ad.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac10efe544a.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac101435582b.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac1070754f14.segments.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150.ac102d2a7986.segments.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac105c222267.segments.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac1062be44c9.segments.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac105fa674d3.calls.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150.ac1072f4d25.calls.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac1073ce6c2e.calls.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac1013512944.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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac105eb72789.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac1039d65cdb.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac101361562.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac103fcc7f.copynumber.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac1013767a1c.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac103e671bb9.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac1014e33aac.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac103201655c.copynumber.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150a.ac1073473f94.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150b.ac1073473f94.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac107a5f5e16.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-2.ac107a5f5e16.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac102d33415.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-002.ac102d33415.copynumber.bed'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac1030367946.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac1073a125a0.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac1073ed480d.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac10ed778f.copynumber.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac1019a55aa8.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac10a8f5f12.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac1056774bfd.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac106d543b6c.copynumber.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150a.ac1052fc2b73.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150b.ac1052fc2b73.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac107f2f5e5f.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-2.ac107f2f5e5f.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac1047133907.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-002.ac1047133907.copynumber.bed'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac10638378e4.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac102de279d.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac10a362020.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac1090e5993.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac103c11e94.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac101e614b9c.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac10466a594.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac10726821cc.segments.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac10a0062fa.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac10458eaef.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac1071263f1b.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac1030566e1f.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac10112426fa.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac106fe41696.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac107ada46bc.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac105bbf51c0.segments.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150a.ac107ea6185c.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150b.ac107ea6185c.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac1068d53394.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-2.ac1068d53394.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac1067886aa0.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-002.ac1067886aa0.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150a.ac105dc07525.segments.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150b.ac105dc07525.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac107184544c.segments.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-2.ac107184544c.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac101c472174.segments.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-002.ac101c472174.segments.bed'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac107f486795.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac102428489.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac10530f39d8.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac10331510c2.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac104ec5138c.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac1025fc2e6a.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac107f6c5c76.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac107f8b298d.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac1077be181b.calls.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac1037f4320b.calls.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac103e1467b.calls.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac1039ed21ec.calls.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac1051863cfc.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac1030fb7df3.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac10a544ba5.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac10cf16476.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac105985428c.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac105eb35e6d.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac102bcd2b92.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac10724046c8.segments.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq.ac1073b44c4d.calls.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%s.ac1049f03c06.calls.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%i.ac101ef54446.calls.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-%03i.ac105efa5003.calls.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150a.ac107b245b65.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150b.ac107b245b65.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac104b386a11.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-2.ac104b386a11.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac104d9414a9.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-002.ac104d9414a9.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150a.ac10402ff4b.segments.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150b.ac10402ff4b.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac102278591c.segments.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-2.ac102278591c.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac106f4a526.segments.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-002.ac106f4a526.segments.bed'
  - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150a.ac1017484f07.calls.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150b.ac1017484f07.calls.bed'
  - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac104766249.calls.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-2.ac104766249.calls.bed'
  - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac1024673162.calls.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-002.ac1024673162.calls.bed'
  - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150a.ac102b93619f.copynumber.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150b.ac102b93619f.copynumber.vcf'
  - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac102a023b8e.copynumber.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-2.ac102a023b8e.copynumber.vcf'
  - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac10719baa.copynumber.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-002.ac10719baa.copynumber.vcf'
  - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150a.ac10443b7d47.segments.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150b.ac10443b7d47.segments.vcf'
  - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac1062baa1a.segments.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-2.ac1062baa1a.segments.vcf'
  - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac102a872ad4.segments.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-002.ac102a872ad4.segments.vcf'
  - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150a.ac105f37799e.calls.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150b.ac105f37799e.calls.vcf'
  - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac101e543d80.calls.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-2.ac101e543d80.calls.vcf'
  - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac1039164dfa.calls.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-002.ac1039164dfa.calls.vcf'
  - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150a.ac102cf0784e.copynumber.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150b.ac102cf0784e.copynumber.seg'
  - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac1039a11c5a.copynumber.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-2.ac1039a11c5a.copynumber.seg'
  - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac1048a624e9.copynumber.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-002.ac1048a624e9.copynumber.seg'
  - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150a.ac1039325fe5.segments.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150b.ac1039325fe5.segments.seg'
  - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac107d2a1cda.segments.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-2.ac107d2a1cda.segments.seg'
  - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac1016ae6c96.segments.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-002.ac1016ae6c96.segments.seg'
  - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150a.ac10433772fd.calls.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-LGG150b.ac10433772fd.calls.seg'
  - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-1.ac104850447.calls.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-2.ac104850447.calls.seg'
  - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-001.ac1037765136.calls.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqC0dk7\QDNAseq-002.ac1037765136.calls.seg'
> 
> message("* exportBins() ... done")
* exportBins() ... done
> 
> proc.time()
   user  system elapsed 
  84.56    1.57   87.25 

QDNAseq.Rcheck/tests_x64/QDNAseq.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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"
39042527732873208.659800195015714219427.4119.9800195013028382427.499.4
Calling iteration1:

optim results
time: 0
minimum: 16445.6418287481
116443.1634295677-0.939948404909672-0.5351158716347190.04999922851584940.1357341814220170.2320391157632851.492692224927890.46336036623653-0.000744748796554230.0111894143724591-0.000962583906213420.3145629342085070.798554843389167
39057577736324208.659.1800195015714219427.4119.9800195013028382427.499.4
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
39057577736324208.659.1800195015714219427.4119.9800195013028382427.499.4
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
39084257957558208.860.8800195015714219427.4119.9800195013028382427.499.4
39084448124304208.862800195015714219427.4119.9800195013028382427.499.4
39084418124298208.862800195015714219427.4119.9800195013028382427.499.4
39084698391313208.864.1800195015714219427.4119.9800195013028382427.499.4
39088968392268208.864.1800195015714219427.4119.9800195013028382427.499.4
39089058392272208.864.1800195015714219427.4119.9800195013028382427.499.4
39089148392276208.864.1800195015714219427.4119.9800195013028382427.499.4
39089238392280208.864.1800195015714219427.4119.9800195013028382427.499.4
39089328392284208.864.1800195015714219427.4119.9800195013028382427.499.4
39089388392287208.864.1800195015714219427.4119.9800195013028382427.499.4
39089578459017208.864.6800195015714219427.4119.9800195013028382427.499.4
39093748459340208.864.6800195015714219427.4119.9800195013028382427.499.4
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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411ca061e47.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c477051a3.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c452788e.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c7e2a3f9d.copynumber.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c7088ca3.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c3626dd6.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c77db6afc.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c33710e.copynumber.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c40ab13fc.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150.411c3de23f6e.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c24076bb.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c72e056e.copynumber.bed'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411cbe4d0a.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c408261f6.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c55578b2.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c3fa26dc3.copynumber.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c26b945fd.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c2caa320d.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c75d23778.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c19ee7267.copynumber.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c62b43ef6.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150.411c1c3f4de6.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c6dd17d8.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c25bc7b85.copynumber.bed'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c796d368c.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c2ec25c8.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c4f534154.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c2e0a29a0.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c2ec74649.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c6ca03c8f.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c76bb29f.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c6b583e0c.segments.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c40464f2a.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c4c0e3829.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c7d514621.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c5a295373.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c6f947623.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c592c421a.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411cbc14677.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c21886652.segments.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c1cfe7098.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150.411c7fb537f8.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c3c9932f1.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c9802d79.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c71f720e5.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150.411c5da72bf0.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411cece3412.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c1a3428e.segments.bed'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c1b942d7.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c51c5353f.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c68384013.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c37841a8a.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c150f6830.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c1a1610b9.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c28113f61.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c3d3d4e3b.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c245527.calls.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c2641146.calls.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c497a11a.calls.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c3fea32c1.calls.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c1a384ce6.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c22be6060.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c15f67f94.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c4e2c4211.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c218d1e0b.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c2df6e97.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c67ed74d6.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c2ea75374.segments.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c750f3f27.calls.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c5024740d.calls.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c7d2b3f1c.calls.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c46842409.calls.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c242a2b42.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150.411c1d2160fa.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c595e1558.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411cfef2f3f.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c1b712e55.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150.411cf0d1e29.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c389bbac.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c209a575c.segments.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c5f1851ce.calls.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150.411c14ca3d78.calls.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c11da67f0.calls.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c40395df9.calls.bed'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c557b190f.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150.411c307f3a5c.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c29754632.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411cf042c84.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c2195df0.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150.411c26166a5b.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c33add31.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c3c386cbc.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411cd8a1d39.calls.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150.411c39bd3d91.calls.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c72532e2.calls.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c4c967138.calls.vcf'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c51d4328.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150.411c7e694f2c.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c5f6550eb.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c70e36de1.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c203a7f1.segments.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150.411c344e45ef.segments.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c2f5992b.segments.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c6c6673.segments.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c3d6e4c39.calls.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150.411c37684b2.calls.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c3cf3a2f.calls.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411cb6d900.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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c2c6a659a.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c7df62ae1.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c75fd3be.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c29c8526d.copynumber.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c6885b22.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c26fa64f9.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c2df81b4f.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c494caf3.copynumber.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150a.411c633611d4.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150b.411c633611d4.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c18bad0e.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-2.411c18bad0e.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c753d708d.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-002.411c753d708d.copynumber.bed'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c3851c9f.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c5e9d7925.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c2f421b47.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c592d21da.copynumber.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c483575d3.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c57fb4780.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c7adf6660.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c5d8940c9.copynumber.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150a.411c13d711c3.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150b.411c13d711c3.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c23636c3.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-2.411c23636c3.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411cea53428.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-002.411cea53428.copynumber.bed'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c3efa66a2.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c561c10f8.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c505630c0.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c5eeb1a01.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c458b18e2.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c506e11d1.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c100b1bbd.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c2fca2d62.segments.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c272d7db9.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c413878fd.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c142476f4.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c13a1458.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c7a32608a.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c6a6c1a02.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c6f194714.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c7994600.segments.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150a.411c37d366e.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150b.411c37d366e.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c27fd2fb9.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-2.411c27fd2fb9.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c3d8252be.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-002.411c3d8252be.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150a.411c4c08b0f.segments.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150b.411c4c08b0f.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c4eaa52b1.segments.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-2.411c4eaa52b1.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c166524cf.segments.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-002.411c166524cf.segments.bed'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c9e2f08.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c1f284e4b.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c45383b54.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c491f2c45.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c8cd1bfd.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c6f632d0f.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c6c60d89.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c112e29f1.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c7016311b.calls.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c6fec37cb.calls.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c21ea23a.calls.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c53956afb.calls.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c24a259d4.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c69391281.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c23022283.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c6fdd2e61.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c33f220e.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c27852549.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c6eb77c33.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c36927d74.segments.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq.411c1de52a4.calls.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%s.411c794e1cce.calls.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%i.411c387c264f.calls.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-%03i.411c6fc65459.calls.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150a.411c6a165de2.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150b.411c6a165de2.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c3dd83acf.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-2.411c3dd83acf.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c6aa9158f.copynumber.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-002.411c6aa9158f.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150a.411c718c1a89.segments.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150b.411c718c1a89.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c239f1c0d.segments.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-2.411c239f1c0d.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c3a8769f.segments.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-002.411c3a8769f.segments.bed'
  - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150a.411c38fb40df.calls.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150b.411c38fb40df.calls.bed'
  - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c467e6b51.calls.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-2.411c467e6b51.calls.bed'
  - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411ced757d8.calls.bed', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-002.411ced757d8.calls.bed'
  - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150a.411c37096da6.copynumber.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150b.411c37096da6.copynumber.vcf'
  - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c431015df.copynumber.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-2.411c431015df.copynumber.vcf'
  - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c64382e52.copynumber.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-002.411c64382e52.copynumber.vcf'
  - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150a.411c6f402af0.segments.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150b.411c6f402af0.segments.vcf'
  - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c608a23dd.segments.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-2.411c608a23dd.segments.vcf'
  - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c46ec3d63.segments.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-002.411c46ec3d63.segments.vcf'
  - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150a.411c71db2.calls.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150b.411c71db2.calls.vcf'
  - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c65ff2a71.calls.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-2.411c65ff2a71.calls.vcf'
  - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c737e1456.calls.vcf', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-002.411c737e1456.calls.vcf'
  - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150a.411c63772ff4.copynumber.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150b.411c63772ff4.copynumber.seg'
  - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c1e8b6a2a.copynumber.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-2.411c1e8b6a2a.copynumber.seg'
  - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c7c5f636e.copynumber.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-002.411c7c5f636e.copynumber.seg'
  - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150a.411c2c7a11b1.segments.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150b.411c2c7a11b1.segments.seg'
  - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c6afd1a4d.segments.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-2.411c6afd1a4d.segments.seg'
  - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c7f16c66.segments.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-002.411c7f16c66.segments.seg'
  - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150a.411c3e4c276d.calls.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-LGG150b.411c3e4c276d.calls.seg'
  - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-1.411c7fdb76a8.calls.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-2.411c7fdb76a8.calls.seg'
  - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=2] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-001.411c45ad11df.calls.seg', 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKEFPam\QDNAseq-002.411c45ad11df.calls.seg'
> 
> message("* exportBins() ... done")
* exportBins() ... done
> 
> proc.time()
   user  system elapsed 
  76.07    1.92   78.71 

QDNAseq.Rcheck/tests_i386/QDNAseq,copyneutral.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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"
38899645528997118.842.2803888812255594245.493.6803888810142676245.477.4
Calling iteration1:

optim results
time: 0
minimum: 16682.0890247004
116682.0890247004-0.825303675797091-0.323169506423803-0.001754401929814960.2970863141060160.5078724084702190.9928769615298530.1100346090918040.0003692713871108020.0111811691191362-0.0001065348234756080.1102701734224670.145866377811007
38914695531314118.842.3803888812255594245.493.6803888810142676245.477.4
Calling iteration2:

optim results
time: 0
minimum: 16682.0888522346
116682.0888522346-0.816384144994661-0.31848916294222-0.00167850977268490.292952991143050.5008064461942260.9819310567480430.1311557982956840.0002223141320088620.01118096583020170.0001872099918784220.1313921659017140.175722206269368
EM algorithm done ...

Computing posterior probabilities for all segments ...

Total time:0minutes

Adjusting segmented data for cellularity ... 

Cellularity sample1: 1

Adjusting normalized data for cellularity ... 

Cellularity sample1: 1

1
38941375734609118.943.8803888812255594245.493.6803888810142676245.477.4
38941565901353118.945.1803888812255594245.493.6803888810142676245.477.4
38941535901349118.945.1803888812255594245.493.6803888810142676245.477.4
38941816168129118.947.1803888812255594245.493.6803888810142676245.477.4
38946086168767118.947.1803888812255594245.493.6803888810142676245.477.4
38946176168770118.947.1803888812255594245.493.6803888810142676245.477.4
38946266168773118.947.1803888812255594245.493.6803888810142676245.477.4
38946356168776118.947.1803888812255594245.493.6803888810142676245.477.4
38946446168779118.947.1803888812255594245.493.6803888810142676245.477.4
38946506168781118.947.1803888812255594245.493.6803888810142676245.477.4
38946696235495118.947.6803888812255594245.493.6803888810142676245.477.4
38950866235732118.947.6803888812255594245.493.6803888810142676245.477.4
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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKKdnib\QDNAseq-%s8c202e887941.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKKdnib\QDNAseq-%s8c2024e36c5a.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKKdnib\QDNAseq-%s8c206c80447c.calls.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKKdnib\QDNAseq-%s8c203d3378b8.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKKdnib\QDNAseq-%s8c204f94128b.segments.igv'
  - exportBins(<1 samples>, format="igv", type="calls")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKKdnib\QDNAseq-%s8c20143b30f9.calls.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKKdnib\QDNAseq-LGG1508c202dee2151.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKKdnib\QDNAseq-LGG1508c20e1c232d.segments.bed'
  - exportBins(<1 samples>, format="bed", type="calls")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKKdnib\QDNAseq-LGG1508c204e605977.calls.bed'
  - exportBins(<1 samples>, format="seg", type="copynumber")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKKdnib\QDNAseq-LGG1508c2076db386d.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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKKdnib\QDNAseq-LGG1508c2020a8103.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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKKdnib\QDNAseq-LGG1508c201cbe1c11.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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKKdnib\QDNAseq-LGG1508c204af27c2c.copynumber.vcf'
character(0)
  - exportBins(<1 samples>, format="vcf", type="segments")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKKdnib\QDNAseq-LGG1508c2069f92323.segments.vcf'
character(0)
  - exportBins(<1 samples>, format="vcf", type="calls")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpKKdnib\QDNAseq-LGG1508c20309e106c.calls.vcf'
character(0)
> 
> proc.time()
   user  system elapsed 
  15.43    0.20   16.06 

QDNAseq.Rcheck/tests_x64/QDNAseq,copyneutral.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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"
38899647726189207.859800573515134256427.6115.5800573510387517427.679.3
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
38914697729610207.959800573515134256427.6115.5800573510387517427.679.3
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
3894137795136420860.7800573515134256427.6115.5800573510466701427.679.9
3894156811811020862800573515134256427.6115.5800573510466701427.679.9
3894153811810420862800573515134256427.6115.5800573510466701427.679.9
3894181838488420864800573515134256427.6115.5800573510466701427.679.9
3894608838583920864800573515134256427.6115.5800573510466701427.679.9
3894617838584320864800573515134256427.6115.5800573510466701427.679.9
3894626838584720864800573515134256427.6115.5800573510466701427.679.9
3894635838585120864800573515134256427.6115.5800573510466701427.679.9
3894644838585520864800573515134256427.6115.5800573510466701427.679.9
3894650838585820864800573515134256427.6115.5800573510466701427.679.9
3894669845258820864.5800573515134256427.6115.5800573510466701427.679.9
38950868452911208.164.5800573515134256427.6115.5800573510466701427.679.9
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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\Rtmpu0AIFR\QDNAseq-%sbcd41206767.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\Rtmpu0AIFR\QDNAseq-%sbcd43abd424.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\Rtmpu0AIFR\QDNAseq-%sbcd417f773.calls.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\Rtmpu0AIFR\QDNAseq-%sbcd468fc1dc0.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\Rtmpu0AIFR\QDNAseq-%sbcd438c029c0.segments.igv'
  - exportBins(<1 samples>, format="igv", type="calls")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\Rtmpu0AIFR\QDNAseq-%sbcd466c22dc9.calls.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\Rtmpu0AIFR\QDNAseq-LGG150bcd43a34390d.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\Rtmpu0AIFR\QDNAseq-LGG150bcd420b3f9a.segments.bed'
  - exportBins(<1 samples>, format="bed", type="calls")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\Rtmpu0AIFR\QDNAseq-LGG150bcd464c13b3e.calls.bed'
  - exportBins(<1 samples>, format="seg", type="copynumber")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\Rtmpu0AIFR\QDNAseq-LGG150bcd43b1724ce.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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\Rtmpu0AIFR\QDNAseq-LGG150bcd435da105d.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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\Rtmpu0AIFR\QDNAseq-LGG150bcd44f054c61.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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\Rtmpu0AIFR\QDNAseq-LGG150bcd448ae22e0.copynumber.vcf'
character(0)
  - exportBins(<1 samples>, format="vcf", type="segments")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\Rtmpu0AIFR\QDNAseq-LGG150bcd450a31513.segments.vcf'
character(0)
  - exportBins(<1 samples>, format="vcf", type="calls")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\Rtmpu0AIFR\QDNAseq-LGG150bcd455a06d2a.calls.vcf'
character(0)
> 
> proc.time()
   user  system elapsed 
  15.85    0.29   16.31 

QDNAseq.Rcheck/tests_i386/QDNAseq,gain-copyneutral-gain.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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"
38902745567054118.842.5803831112255594245.493.6803831110145429245.477.5
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
38944475772492118.944.1803831112255594245.493.6803831110145429245.477.5
38944665939236118.945.4803831112255594245.493.6803831110145429245.477.5
38944635939232118.945.4803831112255594245.493.6803831110145429245.477.5
38944916207762118.947.4803831112255594245.493.6803831110145429245.477.5
38949186208400118.947.4803831112255594245.493.6803831110145429245.477.5
38949276208403118.947.4803831112255594245.493.6803831110145429245.477.5
38949366208406118.947.4803831112255594245.493.6803831110145429245.477.5
38949456208409118.947.4803831112255594245.493.6803831110145429245.477.5
38949546208412118.947.4803831112255594245.493.6803831110145429245.477.5
38949606208414118.947.4803831112255594245.493.6803831110145429245.477.5
38949796275128118.947.9803831112255594245.493.6803831110145429245.477.5
38953966275365118.947.9803831112255594245.493.6803831110145429245.477.5
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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpOEyO2V\QDNAseq-%sc34c59f338d5.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpOEyO2V\QDNAseq-%sc34c8156059.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpOEyO2V\QDNAseq-%sc34c6f003784.calls.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpOEyO2V\QDNAseq-%sc34c7b23a23.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpOEyO2V\QDNAseq-%sc34c71beb5a.segments.igv'
  - exportBins(<1 samples>, format="igv", type="calls")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpOEyO2V\QDNAseq-%sc34c1fb776d.calls.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpOEyO2V\QDNAseq-LGG150c34c33fa7cec.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpOEyO2V\QDNAseq-LGG150c34c4d04701c.segments.bed'
  - exportBins(<1 samples>, format="bed", type="calls")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpOEyO2V\QDNAseq-LGG150c34c3a7b22d4.calls.bed'
  - exportBins(<1 samples>, format="seg", type="copynumber")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpOEyO2V\QDNAseq-LGG150c34c614e4c2f.copynumber.seg'
                                                                                  SAMPLE_NAME
1 D:\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpOEyO2V\\QDNAseq-LGG150c34c614e4c2f.copynumber.seg
2 D:\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpOEyO2V\\QDNAseq-LGG150c34c614e4c2f.copynumber.seg
  CHROMOSOME    START      STOP DATAPOINTS LOG2_RATIO_MEAN
1          7 37110001  68955000       1487            0.99
2          7 90165001 122010000       2012            0.99
  - exportBins(<1 samples>, format="seg", type="segments")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpOEyO2V\QDNAseq-LGG150c34c5df06b2.segments.seg'
                                                                               SAMPLE_NAME
1 D:\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpOEyO2V\\QDNAseq-LGG150c34c5df06b2.segments.seg
2 D:\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpOEyO2V\\QDNAseq-LGG150c34c5df06b2.segments.seg
  CHROMOSOME    START      STOP DATAPOINTS LOG2_RATIO_MEAN
1          7 37110001  68955000       1487            0.99
2          7 90165001 122010000       2012            0.99
  - exportBins(<1 samples>, format="seg", type="calls")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpOEyO2V\QDNAseq-LGG150c34c612560e6.calls.seg'
                                                                             SAMPLE_NAME
1 D:\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpOEyO2V\\QDNAseq-LGG150c34c612560e6.calls.seg
2 D:\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpOEyO2V\\QDNAseq-LGG150c34c612560e6.calls.seg
  CHROMOSOME    START      STOP DATAPOINTS LOG2_RATIO_MEAN
1          7 37110001  68955000       1487            0.99
2          7 90165001 122010000       2012            0.99
  - exportBins(<1 samples>, format="vcf", type="copynumber")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpOEyO2V\QDNAseq-LGG150c34c78261b71.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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpOEyO2V\QDNAseq-LGG150c34c42e6492a.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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpOEyO2V\QDNAseq-LGG150c34c717e68cc.calls.vcf'
  V1       V2 V3    V4    V5   V6   V7
1  7 37110001  . <DIP> <DUP> 1000 PASS
2  7 90165001  . <DIP> <DUP> 1000 PASS
                                                                      V8 V9 V10
1  SVTYPE=DUP;END=68955000;SVLEN=31845000;BINS=1487;SCORE=2;LOG2CNT=0.99 GT 0/1
2 SVTYPE=DUP;END=122010000;SVLEN=31845000;BINS=2012;SCORE=2;LOG2CNT=0.99 GT 0/1
> 
> proc.time()
   user  system elapsed 
  15.98    0.20   16.25 

QDNAseq.Rcheck/tests_x64/QDNAseq,gain-copyneutral-gain.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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"
38902587769768207.859.3800573515139042427.6115.6800573512540766427.695.7
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
3894431799475120861800573515139042427.6115.6800573512540766427.695.7
3894450816149720862.3800573515139042427.6115.6800573512540766427.695.7
3894447816149120862.3800573515139042427.6115.6800573512540766427.695.7
3894475843002120864.4800573515139042427.6115.6800573512540766427.695.7
38949028430976208.164.4800573515139042427.6115.6800573512540766427.695.7
38949118430980208.164.4800573515139042427.6115.6800573512540766427.695.7
38949208430984208.164.4800573515139042427.6115.6800573512540766427.695.7
38949298430988208.164.4800573515139042427.6115.6800573512540766427.695.7
38949388430992208.164.4800573515139042427.6115.6800573512540766427.695.7
38949448430995208.164.4800573515139042427.6115.6800573512540766427.695.7
38949638497725208.164.9800573515139042427.6115.6800573512540766427.695.7
38953808498048208.164.9800573515139042427.6115.6800573512540766427.695.7
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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpURpT6u\QDNAseq-%sc2cc5b455da.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpURpT6u\QDNAseq-%sc2cc7bd95a3d.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpURpT6u\QDNAseq-%sc2cc73bb26ea.calls.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpURpT6u\QDNAseq-%sc2cc5b6b6a2a.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpURpT6u\QDNAseq-%sc2cc43b1871.segments.igv'
  - exportBins(<1 samples>, format="igv", type="calls")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpURpT6u\QDNAseq-%sc2cc3a973ce7.calls.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpURpT6u\QDNAseq-LGG150c2ccd05700.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpURpT6u\QDNAseq-LGG150c2cc524e462a.segments.bed'
  - exportBins(<1 samples>, format="bed", type="calls")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpURpT6u\QDNAseq-LGG150c2cc793c7b9a.calls.bed'
  - exportBins(<1 samples>, format="seg", type="copynumber")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpURpT6u\QDNAseq-LGG150c2cca562bb6.copynumber.seg'
                                                                                 SAMPLE_NAME
1 D:\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpURpT6u\\QDNAseq-LGG150c2cca562bb6.copynumber.seg
2 D:\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpURpT6u\\QDNAseq-LGG150c2cca562bb6.copynumber.seg
  CHROMOSOME    START      STOP DATAPOINTS LOG2_RATIO_MEAN
1          7 37110001  68955000       1487            0.99
2          7 90165001 122010000       2012            0.99
  - exportBins(<1 samples>, format="seg", type="segments")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpURpT6u\QDNAseq-LGG150c2cc317463bb.segments.seg'
                                                                                SAMPLE_NAME
1 D:\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpURpT6u\\QDNAseq-LGG150c2cc317463bb.segments.seg
2 D:\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpURpT6u\\QDNAseq-LGG150c2cc317463bb.segments.seg
  CHROMOSOME    START      STOP DATAPOINTS LOG2_RATIO_MEAN
1          7 37110001  68955000       1487            0.99
2          7 90165001 122010000       2012            0.99
  - exportBins(<1 samples>, format="seg", type="calls")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpURpT6u\QDNAseq-LGG150c2cc70e14d81.calls.seg'
                                                                             SAMPLE_NAME
1 D:\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpURpT6u\\QDNAseq-LGG150c2cc70e14d81.calls.seg
2 D:\\biocbuild\\bbs-3.14-bioc\\tmpdir\\RtmpURpT6u\\QDNAseq-LGG150c2cc70e14d81.calls.seg
  CHROMOSOME    START      STOP DATAPOINTS LOG2_RATIO_MEAN
1          7 37110001  68955000       1487            0.99
2          7 90165001 122010000       2012            0.99
  - exportBins(<1 samples>, format="vcf", type="copynumber")
    File(s) written: [n=1] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpURpT6u\QDNAseq-LGG150c2cc32994a98.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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpURpT6u\QDNAseq-LGG150c2cc50641912.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] 'D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpURpT6u\QDNAseq-LGG150c2cc31dc57a9.calls.vcf'
  V1       V2 V3    V4    V5   V6   V7
1  7 37110001  . <DIP> <DUP> 1000 PASS
2  7 90165001  . <DIP> <DUP> 1000 PASS
                                                                      V8 V9 V10
1  SVTYPE=DUP;END=68955000;SVLEN=31845000;BINS=1487;SCORE=2;LOG2CNT=0.99 GT 0/1
2 SVTYPE=DUP;END=122010000;SVLEN=31845000;BINS=2012;SCORE=2;LOG2CNT=0.99 GT 0/1
> 
> proc.time()
   user  system elapsed 
  15.93    0.42   16.45 

QDNAseq.Rcheck/tests_i386/QDNAseq,parallel-reproducibility.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
> 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))
+   
+   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
There were 50 or more warnings (use warnings() to see the first 50)
> 
> future::plan(oplan)
> 
> proc.time()
   user  system elapsed 
  40.46    0.26   50.12 

QDNAseq.Rcheck/tests_x64/QDNAseq,parallel-reproducibility.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
> 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))
+   
+   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
There were 50 or more warnings (use warnings() to see the first 50)
> 
> future::plan(oplan)
> 
> proc.time()
   user  system elapsed 
  36.59    0.40   43.53 

Example timings

QDNAseq.Rcheck/examples_i386/QDNAseq-Ex.timings

nameusersystemelapsed
addPhenodata0.110.000.11
applyFilters0.120.010.14
binReadCounts000
callBins17.23 0.0617.30
compareToReference1.440.001.44
correctBins1.290.031.32
createBins000
estimateCorrection1.320.001.32
exportBins000
frequencyPlot17.79 0.0217.81
getBinAnnotations000
highlightFilters0.710.040.75
isobarPlot0.890.020.91
makeCgh1.420.001.42
noisePlot1.330.001.33
normalizeBins1.360.001.35
normalizeSegmentedBins10.06 0.0110.08
plot1.940.021.96
poolRuns0.110.000.11
segmentBins10 010
smoothOutlierBins1.380.001.38

QDNAseq.Rcheck/examples_x64/QDNAseq-Ex.timings

nameusersystemelapsed
addPhenodata0.090.000.09
applyFilters0.410.000.41
binReadCounts000
callBins13.89 0.1114.00
compareToReference1.420.041.47
correctBins1.340.021.36
createBins000
estimateCorrection1.280.031.31
exportBins000
frequencyPlot13.82 0.0113.83
getBinAnnotations000
highlightFilters0.600.030.64
isobarPlot0.800.050.84
makeCgh1.410.051.45
noisePlot1.310.011.33
normalizeBins1.360.001.36
normalizeSegmentedBins5.580.035.61
plot1.870.011.89
poolRuns0.100.000.09
segmentBins5.700.035.73
smoothOutlierBins1.370.001.38