Daoud Sie
| Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/QDNAseq |
| git_branch: devel |
| git_last_commit: 2221207 |
| git_last_commit_date: 2024-10-29 09:50:46 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-25 15:39 -0500 (Sat, 25 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4658 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4455 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1622/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| QDNAseq 1.43.0 (landing page) Daoud Sie
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the QDNAseq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/QDNAseq.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: QDNAseq |
| Version: 1.43.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:QDNAseq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings QDNAseq_1.43.0.tar.gz |
| StartedAt: 2025-01-25 10:31:10 -0000 (Sat, 25 Jan 2025) |
| EndedAt: 2025-01-25 10:39:05 -0000 (Sat, 25 Jan 2025) |
| EllapsedTime: 475.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: QDNAseq.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:QDNAseq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings QDNAseq_1.43.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/QDNAseq.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QDNAseq/DESCRIPTION’ ... OK
* this is package ‘QDNAseq’ version ‘1.43.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘QDNAseq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ...Warning: program compiled against libxml 212 using older 211
OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
exportBins.Rd: cghRaw, cghSeg, cghCall, cghRegions
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
callBins 22.715 0.167 22.923
frequencyPlot 22.838 0.003 22.887
normalizeSegmentedBins 8.587 0.004 8.606
segmentBins 8.355 0.004 8.374
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘QDNAseq,copyneutral.R’
Running ‘QDNAseq,gain-copyneutral-gain.R’
Running ‘QDNAseq,parallel-reproducibility.R’
Running ‘QDNAseq.R’
Running ‘binReadCounts.R’
Running ‘poolRuns.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc/meat/QDNAseq.Rcheck/00check.log’
for details.
QDNAseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL QDNAseq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘QDNAseq’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (QDNAseq)
QDNAseq.Rcheck/tests/binReadCounts.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(QDNAseq)
>
> if (requireNamespace("QDNAseq.hg19", quietly = TRUE)) {
+ bins <- getBinAnnotations(500, genome = "hg19")
+ print(bins)
+
+ bam <- system.file("extdata", "ex1.bam", package = "Rsamtools")
+ print(bam)
+
+ counts <- binReadCounts(bins, bamfiles = bam)
+ print(counts)
+
+ ## BUG: https://github.com/ccagc/QDNAseq/issues/89
+ counts2 <- binReadCounts(bins, bamfiles = bam, chunkSize = 10e3)
+ print(counts2)
+ }
Loaded bin annotations for genome 'hg19', bin size 500 kbp, and experiment type 'SR50' from annotation package QDNAseq.hg19 v1.37.0
QDNAseq bin annotations for Hsapiens, build hg19.
Created by Ilari Scheinin with QDNAseq 0.7.5, 2014-02-06 14:20:46.041402.
An object of class 'AnnotatedDataFrame'
rowNames: 1:1-500000 1:500001-1000000 ... Y:59000001-59373566 (6206
total)
varLabels: chromosome start ... use (9 total)
varMetadata: labelDescription
[1] "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rsamtools/extdata/ex1.bam"
ex1 (1 of 1): extracting reads ... binning ...
QDNAseqReadCounts (storageMode: lockedEnvironment)
assayData: 6206 features, 1 samples
element names: counts
protocolData: none
phenoData
sampleNames: ex1
varLabels: name total.reads used.reads expected.variance
varMetadata: labelDescription
featureData
featureNames: 1:1-500000 1:500001-1000000 ... Y:59000001-59373566
(6206 total)
fvarLabels: chromosome start ... use (9 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
ex1 (1 of 1): extracting reads ...
binning chunk - seq1:1:10001
binning chunk - seq2:1:10001
QDNAseqReadCounts (storageMode: lockedEnvironment)
assayData: 6206 features, 1 samples
element names: counts
protocolData: none
phenoData
sampleNames: ex1
varLabels: name total.reads used.reads expected.variance
varMetadata: labelDescription
featureData
featureNames: 1:1-500000 1:500001-1000000 ... Y:59000001-59373566
(6206 total)
fvarLabels: chromosome start ... use (9 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
>
>
>
> proc.time()
user system elapsed
7.929 0.222 8.155
QDNAseq.Rcheck/tests/poolRuns.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(QDNAseq)
> library(Biobase) ## sampleNames()
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> data(LGG150)
>
> message("poolRuns(LGG150) ...")
poolRuns(LGG150) ...
> pooledReadCounts <- poolRuns(LGG150, samples = sampleNames(LGG150))
> print(pooledReadCounts)
QDNAseqReadCounts (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples
element names: counts
protocolData: none
phenoData
sampleNames: LGG150
varLabels: name reads used.reads expected.variance
varMetadata: labelDescription
featureData
featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
(38819 total)
fvarLabels: chromosome start ... use (9 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
> message("poolRuns(LGG150) ... done")
poolRuns(LGG150) ... done
>
>
> message("Create fake data set with two samples ...")
Create fake data set with two samples ...
> phenodata <- phenoData(LGG150)
> phenodata@data <- rbind(phenodata@data, phenodata@data)
>
> counts <- assayDataElement(LGG150, "counts")
> counts2 <- cbind(counts, counts)
> colnames(counts2) <- sampleNames(phenodata)
>
> x <- new("QDNAseqReadCounts", bins = featureData(LGG150), phenodata = phenodata, counts = counts2)
> print(x)
QDNAseqReadCounts (storageMode: lockedEnvironment)
assayData: 38819 features, 2 samples
element names: counts
protocolData: none
phenoData
sampleNames: LGG150 LGG1501
varLabels: name reads used.reads expected.variance
varMetadata: labelDescription
featureData
featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
(38819 total)
fvarLabels: chromosome start ... use (9 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
> message("Create fake data set with two samples ... done")
Create fake data set with two samples ... done
>
> message("poolRuns(LGG150set) ...")
poolRuns(LGG150set) ...
> x_pool <- poolRuns(x, samples = sampleNames(x))
> print(x_pool)
QDNAseqReadCounts (storageMode: lockedEnvironment)
assayData: 38819 features, 2 samples
element names: counts
protocolData: none
phenoData
sampleNames: LGG150 LGG1501
varLabels: name reads used.reads expected.variance
varMetadata: labelDescription
featureData
featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
(38819 total)
fvarLabels: chromosome start ... use (9 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
>
> message("poolRuns(LGG150set) - pooled ...")
poolRuns(LGG150set) - pooled ...
> ## BUG #112 (https://github.com/ccagc/QDNAseq/issues/112)
> x_pool <- poolRuns(x, samples = rep("pooled", times = 2L))
> print(x_pool)
QDNAseqReadCounts (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples
element names: counts
protocolData: none
phenoData
sampleNames: pooled
varLabels: name reads ... total.reads (5 total)
varMetadata: labelDescription
featureData
featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
(38819 total)
fvarLabels: chromosome start ... use (9 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
>
> message("poolRuns(LGG150set) ... done")
poolRuns(LGG150set) ... done
>
> proc.time()
user system elapsed
5.940 0.207 6.145
QDNAseq.Rcheck/tests/QDNAseq,copyneutral.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(QDNAseq)
> library(Biobase)
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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"
39207518080612209.461.7795155415781676424.7120.5795155410837259424.782.7
Calling iteration1:
optim results
time: 0
minimum: 16682.0890247004
116682.0890247004-0.825303675797091-0.323169506423803-0.001754401929814960.2970863141060160.5078724084702190.9928769615298530.1100346090918040.0003692713871108020.0111811691191362-0.0001065348234756080.1102701734224670.145866377811007
39222568084033209.561.7795155415781676424.7120.5795155410837259424.782.7
Calling iteration2:
optim results
time: 0
minimum: 16682.0888522346
116682.0888522346-0.816384144994661-0.31848916294222-0.00167850977268490.292952991143050.5008064461942260.9819310567480430.1311557982956840.0002223141320088620.01118096583020170.0001872099918784220.1313921659017140.175722206269368
EM algorithm done ...
Computing posterior probabilities for all segments ...
Total time:0minutes
Adjusting segmented data for cellularity ...
Cellularity sample1: 1
Adjusting normalized data for cellularity ...
Cellularity sample1: 1
1
39249248305787209.763.4795155415781676424.7120.5795155410837259424.782.7
39249438472533209.764.7795155415781676424.7120.5795155410837259424.782.7
39249408472527209.764.7795155415781676424.7120.5795155410837259424.782.7
39249688739307209.766.7795155415781676424.7120.5795155410837259424.782.7
39253858740241209.766.7795155415781676424.7120.5795155410837259424.782.7
39253948740245209.766.7795155415781676424.7120.5795155410837259424.782.7
39254038740249209.766.7795155415781676424.7120.5795155410837259424.782.7
39254128740253209.766.7795155415781676424.7120.5795155410837259424.782.7
39254218740257209.766.7795155415781676424.7120.5795155410837259424.782.7
39254278740260209.766.7795155415781676424.7120.5795155410837259424.782.7
39254468806990209.767.2795155415781676424.7120.5795155410837259424.782.7
39258638807313209.767.2795155415781676424.7120.5795155410837259424.782.7
FINISHED!
Total time:0minutes
There were 24 warnings (use warnings() to see them)
> print(fitC)
QDNAseqCopyNumbers (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples
element names: calls, copynumber, probamp, probdloss, probgain, probloss, probnorm, segmented
protocolData: none
phenoData
sampleNames: LGG150
varLabels: name reads ... loess.family (6 total)
varMetadata: labelDescription
featureData
featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
(38819 total)
fvarLabels: chromosome start ... use (9 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
>
>
> ## Assert that everything is called copy-neutral
> calls <- assayDataElement(fitC, "calls")
> stopifnot(all(is.na(calls) | calls == 0))
>
> formats <- c("tsv", "igv", "bed", "seg", "vcf")
> types <- c("copynumber", "segments", "calls")
> for (format in formats) {
+ for (type in types) {
+ fileext <- sprintf(".%s.%s", type, format)
+ file <- tempfile(pattern = "QDNAseq-%s", fileext = fileext)
+ message(sprintf(" - exportBins(<%d samples>, format=\"%s\", type=\"%s\")", ncol(fitC), format, type))
+ file <- exportBins(fitC, format = format, type = type, file = file)
+ message(sprintf(" File(s) written: [n=%d] %s",
+ length(file), paste(sQuote(file), collapse = ", ")))
+ stopifnot(all(file_test("-f", file)))
+ if (format == "seg") {
+ segs <- read.table(file, sep = "\t", header = TRUE)
+ print(segs)
+ stopifnot(nrow(segs) == 0L)
+ } else if (format == "vcf") {
+ rows <- readLines(file)
+ rows <- grep("^#", rows, invert = TRUE, value = TRUE)
+ print(rows)
+ stopifnot(length(rows) == 0L)
+ }
+ file.remove(file)
+ stopifnot(!any(file_test("-f", file)))
+ }
+ }
- exportBins(<1 samples>, format="tsv", type="copynumber")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPJj4H/QDNAseq-%s36c0617184ebe4.copynumber.tsv'
- exportBins(<1 samples>, format="tsv", type="segments")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPJj4H/QDNAseq-%s36c061298a7473.segments.tsv'
- exportBins(<1 samples>, format="tsv", type="calls")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPJj4H/QDNAseq-%s36c0613f094998.calls.tsv'
- exportBins(<1 samples>, format="igv", type="copynumber")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPJj4H/QDNAseq-%s36c0613aba41b6.copynumber.igv'
- exportBins(<1 samples>, format="igv", type="segments")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPJj4H/QDNAseq-%s36c0613563eca6.segments.igv'
- exportBins(<1 samples>, format="igv", type="calls")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPJj4H/QDNAseq-%s36c0612a7b4181.calls.igv'
- exportBins(<1 samples>, format="bed", type="copynumber")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPJj4H/QDNAseq-LGG15036c06128aab0ee.copynumber.bed'
- exportBins(<1 samples>, format="bed", type="segments")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPJj4H/QDNAseq-LGG15036c0615d9d3296.segments.bed'
- exportBins(<1 samples>, format="bed", type="calls")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPJj4H/QDNAseq-LGG15036c0617649d4ca.calls.bed'
- exportBins(<1 samples>, format="seg", type="copynumber")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPJj4H/QDNAseq-LGG15036c0615caccb4f.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] '/home/biocbuild/tmp/RtmpyPJj4H/QDNAseq-LGG15036c0616a01e689.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] '/home/biocbuild/tmp/RtmpyPJj4H/QDNAseq-LGG15036c061132e06f8.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] '/home/biocbuild/tmp/RtmpyPJj4H/QDNAseq-LGG15036c0614118c74f.copynumber.vcf'
character(0)
- exportBins(<1 samples>, format="vcf", type="segments")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPJj4H/QDNAseq-LGG15036c06133712285.segments.vcf'
character(0)
- exportBins(<1 samples>, format="vcf", type="calls")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPJj4H/QDNAseq-LGG15036c06169ad0849.calls.vcf'
character(0)
>
> proc.time()
user system elapsed
24.137 0.275 24.444
QDNAseq.Rcheck/tests/QDNAseq,gain-copyneutral-gain.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(QDNAseq)
> library(Biobase)
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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"
39210618124191209.562795155415781676424.7120.5795155410837055424.782.7
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
39252348349174209.763.7795155415781676424.7120.5795155410866073424.783
39252538515920209.765795155415781676424.7120.5795155410866073424.783
39252508515914209.765795155415781676424.7120.5795155410866073424.783
39252788784444209.767.1795155415781676424.7120.5795155410866073424.783
39256958785378209.767.1795155415781676424.7120.5795155410866073424.783
39257048785382209.767.1795155415781676424.7120.5795155410866073424.783
39257138785386209.767.1795155415781676424.7120.5795155410866073424.783
39257228785390209.767.1795155415781676424.7120.5795155410866073424.783
39257318785394209.767.1795155415781676424.7120.5795155410866073424.783
39257378785397209.767.1795155415781676424.7120.5795155410866073424.783
39257568852127209.767.6795155415781676424.7120.5795155410866073424.783
39261738852450209.767.6795155415781676424.7120.5795155410866073424.783
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] '/home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-%s36c43b7a2c4472.copynumber.tsv'
- exportBins(<1 samples>, format="tsv", type="segments")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-%s36c43b1ee1409c.segments.tsv'
- exportBins(<1 samples>, format="tsv", type="calls")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-%s36c43b13461983.calls.tsv'
- exportBins(<1 samples>, format="igv", type="copynumber")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-%s36c43b5e5948d5.copynumber.igv'
- exportBins(<1 samples>, format="igv", type="segments")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-%s36c43b25dc32fb.segments.igv'
- exportBins(<1 samples>, format="igv", type="calls")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-%s36c43b5cf21c3b.calls.igv'
- exportBins(<1 samples>, format="bed", type="copynumber")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-LGG15036c43b2ba913b5.copynumber.bed'
- exportBins(<1 samples>, format="bed", type="segments")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-LGG15036c43b628b2d89.segments.bed'
- exportBins(<1 samples>, format="bed", type="calls")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-LGG15036c43b5eae258a.calls.bed'
- exportBins(<1 samples>, format="seg", type="copynumber")
File(s) written: [n=1] '/home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-LGG15036c43b65e02d81.copynumber.seg'
SAMPLE_NAME
1 /home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-LGG15036c43b65e02d81.copynumber.seg
2 /home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-LGG15036c43b65e02d81.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] '/home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-LGG15036c43b623e5cab.segments.seg'
SAMPLE_NAME
1 /home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-LGG15036c43b623e5cab.segments.seg
2 /home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-LGG15036c43b623e5cab.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] '/home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-LGG15036c43b311d7843.calls.seg'
SAMPLE_NAME
1 /home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-LGG15036c43b311d7843.calls.seg
2 /home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-LGG15036c43b311d7843.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] '/home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-LGG15036c43b1d9d79df.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] '/home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-LGG15036c43b445ce513.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] '/home/biocbuild/tmp/RtmpyPc2fO/QDNAseq-LGG15036c43b5954a4da.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
25.686 0.333 26.059
QDNAseq.Rcheck/tests/QDNAseq,parallel-reproducibility.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> ######################################################################
> # This scripts asserts that for each processing step of QDNAseq
> # the output/results are reproducible (numerically equal).
> ######################################################################
> library("QDNAseq")
> options("QDNAseq::verbose"=FALSE)
>
> # Load data
> data(LGG150)
> data <- LGG150
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # TRUTH
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Filter out "bad" bins
> dataF <- applyFilters(data, residual=TRUE, blacklist=TRUE)
>
> # Correct read counts as a function of GC content and mappability
> dataC <- correctBins(dataF)
>
> # Normalize binned read counts to have diploid normal copy number
> dataN <- normalizeBins(dataC)
>
> # Segment copy numbers
> set.seed(42) ## segmentBins() relies on RNG via DNAcopy::segment()
> fit <- segmentBins(dataN)
>
> # Call copy-number segments
> fitC <- callBins(fit)
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # REPRODUCIBILITY
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> strategies <- c("sequential", "multisession")
> if (parallelly::supportsMulticore()) strategies <- c(strategies, "multicore")
>
> oplan <- future::plan("list")
> for (strategy in strategies) {
+ message(sprintf("Reproducibility with plan(\"%s\") ...", strategy))
+
+ future::plan(strategy)
+
+ dataFr <- applyFilters(data, residual=TRUE, blacklist=TRUE)
+ stopifnot(all.equal(dataFr, dataF))
+
+ dataCr <- correctBins(dataF)
+ stopifnot(all.equal(dataCr, dataC))
+
+ dataNr <- normalizeBins(dataC)
+ stopifnot(all.equal(dataNr, dataN))
+
+ set.seed(42) ## segmentBins() relies on RNG via DNAcopy::segment()
+ fitr <- segmentBins(dataNr)
+ stopifnot(all.equal(fitr, fit))
+
+ fitCr <- callBins(fitr)
+ stopifnot(all.equal(fitCr, fitC))
+
+ message(sprintf("Reproducibility with plan(\"%s\") ... done", strategy))
+ }
Reproducibility with plan("sequential") ...
Reproducibility with plan("sequential") ... done
Reproducibility with plan("multisession") ...
Calculating fit for sample LGG150 (1 of 1) ...
Segmenting: LGG150 (1 of 1) ...
Reproducibility with plan("multisession") ... done
Reproducibility with plan("multicore") ...
Reproducibility with plan("multicore") ... done
There were 50 or more warnings (use warnings() to see the first 50)
>
> future::plan(oplan)
>
> proc.time()
user system elapsed
84.028 1.995 97.059
QDNAseq.Rcheck/tests/QDNAseq.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(QDNAseq)
> library(Biobase) ## combine(), sampleNames()
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> library(utils)
>
> do_plot <- TRUE
> do_cleanup <- TRUE
>
> # Load data
> data(LGG150)
> data <- LGG150
> print(data)
QDNAseqReadCounts (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples
element names: counts
protocolData: none
phenoData
sampleNames: LGG150
varLabels: name reads used.reads expected.variance
varMetadata: labelDescription
featureData
featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
(38819 total)
fvarLabels: chromosome start ... use (9 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
> stopifnot(inherits(data, "QDNAseqReadCounts"))
>
> # Plot isobars of read counts
> if (do_plot) isobarPlot(data)
Plotting sample LGG150 median read counts
>
> # Plot copy number profile
> if (do_plot) {
+ plot(data, ylim=c(-100, 200))
+ highlightFilters(data, residual=TRUE, blacklist=TRUE)
+ }
Plotting sample LGG150 (1 of 1) ...
Highlighted 3,375 bins.
>
> # Filter out "bad" bins
> dataF <- applyFilters(data, residual=TRUE, blacklist=TRUE)
38,819 total bins
38,819 of which in selected chromosomes
36,722 of which with reference sequence
33,347 final bins
> print(dataF)
QDNAseqReadCounts (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples
element names: counts
protocolData: none
phenoData
sampleNames: LGG150
varLabels: name reads used.reads expected.variance
varMetadata: labelDescription
featureData
featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
(38819 total)
fvarLabels: chromosome start ... use (9 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
> if (do_plot) plot(dataF, ylim=c(-100, 200))
Plotting sample LGG150 (1 of 1) ...
> stopifnot(inherits(dataF, "QDNAseqReadCounts"))
>
> # Correct read counts as a function of GC content and mappability
> dataC <- correctBins(dataF)
Calculating correction for GC content and mappability
Calculating fit for sample LGG150 (1 of 1) ...
Done.
> print(dataC)
QDNAseqCopyNumbers (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples
element names: copynumber
protocolData: none
phenoData
sampleNames: LGG150
varLabels: name reads ... loess.family (6 total)
varMetadata: labelDescription
featureData
featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
(38819 total)
fvarLabels: chromosome start ... use (9 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
> if (do_plot) plot(dataC, ylim=c(-100, 200))
Plotting sample LGG150 (1 of 1) ...
> stopifnot(inherits(dataC, "QDNAseqCopyNumbers"))
>
> # Normalize binned read counts to have diploid normal copy number
> dataN <- normalizeBins(dataC)
Applying median normalization ...
> print(dataN)
QDNAseqCopyNumbers (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples
element names: copynumber
protocolData: none
phenoData
sampleNames: LGG150
varLabels: name reads ... loess.family (6 total)
varMetadata: labelDescription
featureData
featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
(38819 total)
fvarLabels: chromosome start ... use (9 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
> if (do_plot) plot(dataN)
Plotting sample LGG150 (1 of 1) ...
> stopifnot(inherits(dataN, "QDNAseqCopyNumbers"))
>
> # Plot noise
> if (do_plot) noisePlot(dataF)
Calculating correction for GC content and mappability
Calculating fit for sample LGG150 (1 of 1) ...
Done.
>
> # Segment copy numbers
> fit <- segmentBins(dataN)
Performing segmentation:
Segmenting: LGG150 (1 of 1) ...
> print(fit)
QDNAseqCopyNumbers (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples
element names: copynumber, segmented
protocolData: none
phenoData
sampleNames: LGG150
varLabels: name reads ... loess.family (6 total)
varMetadata: labelDescription
featureData
featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
(38819 total)
fvarLabels: chromosome start ... use (9 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
> if (do_plot) plot(fit)
Plotting sample LGG150 (1 of 1) ...
> stopifnot(inherits(fit, "QDNAseqCopyNumbers"))
>
> # Call copy-number segments
> fitC <- callBins(fit)
EM algorithm started ...
[1] "Total number of segments present in the data: 10"
[1] "Number of segments used for fitting the model: 9"
39351438087454210.261.8776190215371622414.6117.3776190212743019414.697.3
Calling iteration1:
optim results
time: 0
minimum: 16445.6418287481
116443.1634295677-0.939948404909649-0.5351158716346960.04999922851584940.1357341814220170.2320391157632851.492692224927890.46336036623653-0.0007447487965527160.0111894143724591-0.000962583906213420.3145629342085070.798554843389167
39366488090905210.361.8776190215371622414.6117.3776190212743019414.697.3
Calling iteration2:
optim results
time: 0
minimum: 16445.5781374328
116443.1331012469-0.932876677515068-0.5359433038809750.0499979048415910.1114729434735370.1905642555481931.861013902305770.4314700360573740.0001440687684088850.01118427659401560.0007568920162792620.2061088124299370.874022351578009
39366478090904210.361.8776190215371622414.6117.3776190212743019414.697.3
Calling iteration3:
optim results
time: 0
minimum: 16445.5975371627
116443.1273697069-0.924012853099585-0.5365177469718710.04999923288882760.108573194240180.1856071014916831.753751992204390.4694950401327692.93313204153227e-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
39393168312139210.463.5776190215371622414.6117.3776190212743019414.697.3
39393358478885210.464.7776190215371622414.6117.3776190212743019414.697.3
39393328478879210.464.7776190215371622414.6117.3776190212743019414.697.3
39393608745894210.466.8776190215371622414.6117.3776190212743019414.697.3
39397778746828210.566.8776190215371622414.6117.3776190212743019414.697.3
39397868746832210.566.8776190215371622414.6117.3776190212743019414.697.3
39397958746836210.566.8776190215371622414.6117.3776190212743019414.697.3
39398048746840210.566.8776190215371622414.6117.3776190212743019414.697.3
39398138746844210.566.8776190215371622414.6117.3776190212743019414.697.3
39398198746847210.566.8776190215371622414.6117.3776190212743019414.697.3
39398388813577210.567.3776190215371622414.6117.3776190212743019414.697.3
39402558813900210.567.3776190215371622414.6117.3776190212743019414.697.3
FINISHED!
Total time:0minutes
There were 50 or more warnings (use warnings() to see the first 50)
> print(fitC)
QDNAseqCopyNumbers (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples
element names: calls, copynumber, probamp, probdloss, probgain, probloss, probnorm, segmented
protocolData: none
phenoData
sampleNames: LGG150
varLabels: name reads ... loess.family (6 total)
varMetadata: labelDescription
featureData
featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
(38819 total)
fvarLabels: chromosome start ... use (9 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
> if (do_plot) plot(fitC)
Plotting sample LGG150 (1 of 1) ...
>
>
> # ---------------------------------------------------------------
> # Exporting
> # ---------------------------------------------------------------
> message("* exportBins() ...")
* exportBins() ...
>
> sets <- list(data = data, dataC = dataC, fit = fit, fitC = fitC)
> for (name in names(sets)) {
+ set <- sets[[name]]
+ formats <- c("tsv", "igv", "bed")
+ if (name == "fitC") formats <- c(formats, "vcf", "seg")
+ for (format in formats) {
+ types <- c("copynumber")
+ if (name %in% c("fit", "fitC")) types <- c(types, "segments")
+ if (name == "fitC") types <- c(types, "calls")
+ for (type in types) {
+ fileext <- sprintf(".%s.%s", type, format)
+ templates <- c("QDNAseq-%s.", "QDNAseq-%i.", "QDNAseq-%03i.")
+ if (ncol(set) == 1L || !(format %in% c("bed", "seg", "vcf"))) {
+ templates <- c("QDNAseq.", templates)
+ }
+ for (template in templates) {
+ file <- tempfile(pattern = template, fileext = fileext)
+ message(sprintf(" - exportBins(<%d samples>, format=\"%s\", type=\"%s\", file=\"%s\")", ncol(set), format, type, template))
+ file <- exportBins(set, file = file, format = format, type = type)
+ message(sprintf(" File(s) written: [n=%d] %s",
+ length(file), paste(sQuote(file), collapse = ", ")))
+ stopifnot(all(file_test("-f", file)))
+ if (do_cleanup) {
+ file.remove(file)
+ stopifnot(!any(file_test("-f", file)))
+ }
+ }
+ }
+ }
+ }
- exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a7a076fb1.copynumber.tsv'
- exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a4c8a8de1.copynumber.tsv'
- exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a241de714.copynumber.tsv'
- exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a1d0e4b4c.copynumber.tsv'
- exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a490ec940.copynumber.igv'
- exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a786a4df.copynumber.igv'
- exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a4452f36a.copynumber.igv'
- exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a61d3d91.copynumber.igv'
- exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a126effa0.copynumber.bed'
- exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150.36de3a362aba8b.copynumber.bed'
- exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a70260a52.copynumber.bed'
- exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a1f998324.copynumber.bed'
- exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a36f1a114.copynumber.tsv'
- exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a3aa19ee.copynumber.tsv'
- exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a5bd0ccc0.copynumber.tsv'
- exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a20420f6c.copynumber.tsv'
- exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a7b0134e9.copynumber.igv'
- exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a3694de2e.copynumber.igv'
- exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a3938e6b1.copynumber.igv'
- exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a2266f99c.copynumber.igv'
- exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a64557c84.copynumber.bed'
- exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150.36de3a6d4fb872.copynumber.bed'
- exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a2199b777.copynumber.bed'
- exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3ad847cf7.copynumber.bed'
- exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a27a4e21b.copynumber.tsv'
- exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a59ec622c.copynumber.tsv'
- exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a1b16ce4.copynumber.tsv'
- exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a27240144.copynumber.tsv'
- exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a5a79e2e7.segments.tsv'
- exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a1a58f91a.segments.tsv'
- exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a60027bf8.segments.tsv'
- exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a54815298.segments.tsv'
- exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a66e386fb.copynumber.igv'
- exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a420630c.copynumber.igv'
- exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a718f9de5.copynumber.igv'
- exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a2ff2503c.copynumber.igv'
- exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3aba707eb.segments.igv'
- exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a35e2914f.segments.igv'
- exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a360f8dcd.segments.igv'
- exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a1e16078b.segments.igv'
- exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a6c0d4bda.copynumber.bed'
- exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150.36de3a26359820.copynumber.bed'
- exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a3daf8ab0.copynumber.bed'
- exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a22feecee.copynumber.bed'
- exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a29dfb20e.segments.bed'
- exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150.36de3a19805770.segments.bed'
- exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a4340fc5a.segments.bed'
- exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a24e0e6f8.segments.bed'
- exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a5015359e.copynumber.tsv'
- exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a7c79e30b.copynumber.tsv'
- exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a4747e094.copynumber.tsv'
- exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a346ab222.copynumber.tsv'
- exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a69c99b7d.segments.tsv'
- exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a68e1980b.segments.tsv'
- exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a41ef2f19.segments.tsv'
- exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a116e7d98.segments.tsv'
- exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a42cdfa38.calls.tsv'
- exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a43a09bfe.calls.tsv'
- exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a38927edc.calls.tsv'
- exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a1d47dd1f.calls.tsv'
- exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a5df99518.copynumber.igv'
- exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a1894fad4.copynumber.igv'
- exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a71c92fb8.copynumber.igv'
- exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a44dd1c14.copynumber.igv'
- exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a1cb55de0.segments.igv'
- exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a6358cd9d.segments.igv'
- exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a74cf6c50.segments.igv'
- exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a285c65cc.segments.igv'
- exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a193b5eec.calls.igv'
- exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a2adefa1d.calls.igv'
- exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a46726d57.calls.igv'
- exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a548aac6.calls.igv'
- exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a5114923d.copynumber.bed'
- exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150.36de3a421f807.copynumber.bed'
- exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a284797b4.copynumber.bed'
- exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a7af4444c.copynumber.bed'
- exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a1da24f77.segments.bed'
- exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150.36de3a6b88940f.segments.bed'
- exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a1fd52b44.segments.bed'
- exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a6db78515.segments.bed'
- exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a6802771a.calls.bed'
- exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150.36de3a671d0bd8.calls.bed'
- exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a22223737.calls.bed'
- exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a51cc1298.calls.bed'
- exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a4ffea3e4.copynumber.vcf'
- exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150.36de3a64116651.copynumber.vcf'
- exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a633a9030.copynumber.vcf'
- exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a12cc9e1c.copynumber.vcf'
- exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a27b2024f.segments.vcf'
- exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150.36de3a1bcd0f0d.segments.vcf'
- exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a30147b3b.segments.vcf'
- exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a5ab9767.segments.vcf'
- exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a346209e1.calls.vcf'
- exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150.36de3a21ddaaf3.calls.vcf'
- exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a4a88b37b.calls.vcf'
- exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a511767c2.calls.vcf'
- exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a5367890.copynumber.seg'
- exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150.36de3a3f581fcb.copynumber.seg'
- exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a7973cd8e.copynumber.seg'
- exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a1e71d77c.copynumber.seg'
- exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a6a3719e9.segments.seg'
- exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150.36de3a3fe63ae5.segments.seg'
- exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a23ba8242.segments.seg'
- exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a3b4bac26.segments.seg'
- exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a440832ed.calls.seg'
- exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150.36de3a4c0219f7.calls.seg'
- exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a363ff072.calls.seg'
- exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a61aa8264.calls.seg'
>
> sets <- list(data = data, dataC = dataC, fit = fit, fitC = fitC)
> sets <- lapply(sets, FUN = function(set) {
+ stopifnot(ncol(set) == 1L)
+ name <- sampleNames(set)
+ setA <- set
+ sampleNames(setA) <- sprintf("%sa", name)
+ setB <- set
+ sampleNames(setB) <- sprintf("%sb", name)
+ combine(setA, setB)
+ })
>
> for (name in names(sets)) {
+ set <- sets[[name]]
+ stopifnot(ncol(set) == 2L)
+ formats <- c("tsv", "igv", "bed")
+ if (name == "fitC") formats <- c(formats, "vcf", "seg")
+ for (format in formats) {
+ types <- c("copynumber")
+ if (name %in% c("fit", "fitC")) types <- c(types, "segments")
+ if (name == "fitC") types <- c(types, "calls")
+ for (type in types) {
+ fileext <- sprintf(".%s.%s", type, format)
+ templates <- c("QDNAseq-%s.", "QDNAseq-%i.", "QDNAseq-%03i.")
+ if (ncol(set) == 1L || !(format %in% c("bed", "seg", "vcf"))) {
+ templates <- c("QDNAseq.", templates)
+ }
+ for (template in templates) {
+ file <- tempfile(pattern = template, fileext = fileext)
+ message(sprintf(" - exportBins(<%d samples>, format=\"%s\", type=\"%s\", file=\"%s\")", ncol(set), format, type, template))
+ file <- exportBins(set, file = file, format = format, type = type)
+ message(sprintf(" File(s) written: [n=%d] %s",
+ length(file), paste(sQuote(file), collapse = ", ")))
+ stopifnot(all(file_test("-f", file)))
+ if (do_cleanup) {
+ file.remove(file)
+ stopifnot(!any(file_test("-f", file)))
+ }
+ }
+ }
+ }
+ }
- exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a378aae06.copynumber.tsv'
- exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a56151bb6.copynumber.tsv'
- exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a4f62077a.copynumber.tsv'
- exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a1f8d2520.copynumber.tsv'
- exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a3d32278f.copynumber.igv'
- exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a71843eb1.copynumber.igv'
- exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a715937b8.copynumber.igv'
- exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3ad30cb73.copynumber.igv'
- exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150a.36de3a5595a502.copynumber.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150b.36de3a5595a502.copynumber.bed'
- exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a5493c7e9.copynumber.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-2.36de3a5493c7e9.copynumber.bed'
- exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a1ffd698f.copynumber.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-002.36de3a1ffd698f.copynumber.bed'
- exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a7d47a751.copynumber.tsv'
- exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a7060d6f6.copynumber.tsv'
- exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a5011e4ca.copynumber.tsv'
- exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a2f33eb9.copynumber.tsv'
- exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a24c2e0d7.copynumber.igv'
- exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a71ef8fbe.copynumber.igv'
- exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a4d7bf234.copynumber.igv'
- exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a75da4899.copynumber.igv'
- exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150a.36de3a7726084e.copynumber.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150b.36de3a7726084e.copynumber.bed'
- exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3acd41200.copynumber.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-2.36de3acd41200.copynumber.bed'
- exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a6f4e1627.copynumber.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-002.36de3a6f4e1627.copynumber.bed'
- exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a1597dfcb.copynumber.tsv'
- exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a770b2be9.copynumber.tsv'
- exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a2f34510d.copynumber.tsv'
- exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a3952620d.copynumber.tsv'
- exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a3256d80f.segments.tsv'
- exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a733c83fa.segments.tsv'
- exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a5547c04.segments.tsv'
- exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a6896c882.segments.tsv'
- exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a54e7065e.copynumber.igv'
- exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a3cdf2a0a.copynumber.igv'
- exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a3eabe438.copynumber.igv'
- exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a24490dd8.copynumber.igv'
- exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a5c6c4f2b.segments.igv'
- exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a7bde0bc7.segments.igv'
- exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a15cd4c8a.segments.igv'
- exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a4dc586e3.segments.igv'
- exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150a.36de3a90ed73a.copynumber.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150b.36de3a90ed73a.copynumber.bed'
- exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a6b62f18c.copynumber.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-2.36de3a6b62f18c.copynumber.bed'
- exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a22594ecc.copynumber.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-002.36de3a22594ecc.copynumber.bed'
- exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%s.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150a.36de3a290c40c9.segments.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150b.36de3a290c40c9.segments.bed'
- exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a68aa98de.segments.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-2.36de3a68aa98de.segments.bed'
- exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a12ba25c2.segments.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-002.36de3a12ba25c2.segments.bed'
- exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a791e2594.copynumber.tsv'
- exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a6b9dd797.copynumber.tsv'
- exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a377d069a.copynumber.tsv'
- exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a6b0db552.copynumber.tsv'
- exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a3919c9cb.segments.tsv'
- exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a2d574f33.segments.tsv'
- exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a6233bda0.segments.tsv'
- exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a45eddbcb.segments.tsv'
- exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a1ca5655b.calls.tsv'
- exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a77cb9d6b.calls.tsv'
- exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a3cf907b4.calls.tsv'
- exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a4bd9b668.calls.tsv'
- exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a311dff79.copynumber.igv'
- exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a6f4fdfc4.copynumber.igv'
- exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a3f163a62.copynumber.igv'
- exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a36727b7d.copynumber.igv'
- exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a57e6a846.segments.igv'
- exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a13fd40c0.segments.igv'
- exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a7351a588.segments.igv'
- exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a16928c7e.segments.igv'
- exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq.36de3a38464e99.calls.igv'
- exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%s.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%s.36de3a4fbdf4b3.calls.igv'
- exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%i.36de3a12709846.calls.igv'
- exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%03i.")
File(s) written: [n=1] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-%03i.36de3a4e139b23.calls.igv'
- exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150a.36de3a1d837b96.copynumber.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150b.36de3a1d837b96.copynumber.bed'
- exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a1b7f6f80.copynumber.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-2.36de3a1b7f6f80.copynumber.bed'
- exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a39768caf.copynumber.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-002.36de3a39768caf.copynumber.bed'
- exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%s.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150a.36de3a3fdcca63.segments.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150b.36de3a3fdcca63.segments.bed'
- exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a448bb04a.segments.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-2.36de3a448bb04a.segments.bed'
- exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a2221258d.segments.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-002.36de3a2221258d.segments.bed'
- exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%s.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150a.36de3a5296f025.calls.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150b.36de3a5296f025.calls.bed'
- exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a3da9d5de.calls.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-2.36de3a3da9d5de.calls.bed'
- exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%03i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3adbefd24.calls.bed', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-002.36de3adbefd24.calls.bed'
- exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150a.36de3aa13f6bf.copynumber.vcf', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150b.36de3aa13f6bf.copynumber.vcf'
- exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a28b78b30.copynumber.vcf', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-2.36de3a28b78b30.copynumber.vcf'
- exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a46d8c6f0.copynumber.vcf', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-002.36de3a46d8c6f0.copynumber.vcf'
- exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%s.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150a.36de3a376b45f3.segments.vcf', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150b.36de3a376b45f3.segments.vcf'
- exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3aaeb48d0.segments.vcf', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-2.36de3aaeb48d0.segments.vcf'
- exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%03i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3acc6a2bb.segments.vcf', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-002.36de3acc6a2bb.segments.vcf'
- exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%s.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150a.36de3a5410ab4e.calls.vcf', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150b.36de3a5410ab4e.calls.vcf'
- exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a2b6e63c.calls.vcf', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-2.36de3a2b6e63c.calls.vcf'
- exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%03i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a49bfaa70.calls.vcf', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-002.36de3a49bfaa70.calls.vcf'
- exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%s.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150a.36de3a1fea61b6.copynumber.seg', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150b.36de3a1fea61b6.copynumber.seg'
- exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a33d4e5b5.copynumber.seg', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-2.36de3a33d4e5b5.copynumber.seg'
- exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%03i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a390f8a34.copynumber.seg', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-002.36de3a390f8a34.copynumber.seg'
- exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%s.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150a.36de3a5f009c18.segments.seg', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150b.36de3a5f009c18.segments.seg'
- exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a6a476132.segments.seg', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-2.36de3a6a476132.segments.seg'
- exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%03i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a10f6327a.segments.seg', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-002.36de3a10f6327a.segments.seg'
- exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%s.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150a.36de3a72fddcd8.calls.seg', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-LGG150b.36de3a72fddcd8.calls.seg'
- exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-1.36de3a5d9906ba.calls.seg', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-2.36de3a5d9906ba.calls.seg'
- exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%03i.")
File(s) written: [n=2] '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-001.36de3a2788bef8.calls.seg', '/home/biocbuild/tmp/Rtmp523ZHY/QDNAseq-002.36de3a2788bef8.calls.seg'
>
> message("* exportBins() ... done")
* exportBins() ... done
>
> proc.time()
user system elapsed
77.209 0.792 78.153
QDNAseq.Rcheck/QDNAseq-Ex.timings
| name | user | system | elapsed | |
| addPhenodata | 0.121 | 0.004 | 0.124 | |
| applyFilters | 0.367 | 0.004 | 0.372 | |
| binReadCounts | 0 | 0 | 0 | |
| callBins | 22.715 | 0.167 | 22.923 | |
| compareToReference | 2.715 | 0.024 | 2.745 | |
| correctBins | 2.931 | 0.004 | 2.941 | |
| createBins | 0 | 0 | 0 | |
| estimateCorrection | 2.395 | 0.000 | 2.402 | |
| exportBins | 0 | 0 | 0 | |
| frequencyPlot | 22.838 | 0.003 | 22.887 | |
| getBinAnnotations | 0 | 0 | 0 | |
| highlightFilters | 0.718 | 0.004 | 0.723 | |
| isobarPlot | 1.186 | 0.012 | 1.200 | |
| makeCgh | 2.691 | 0.004 | 2.702 | |
| noisePlot | 2.459 | 0.000 | 2.464 | |
| normalizeBins | 2.536 | 0.000 | 2.542 | |
| normalizeSegmentedBins | 8.587 | 0.004 | 8.606 | |
| plot | 3.181 | 0.016 | 3.204 | |
| poolRuns | 0.142 | 0.000 | 0.143 | |
| segmentBins | 8.355 | 0.004 | 8.374 | |
| smoothOutlierBins | 2.585 | 0.008 | 2.598 | |