PureCN: Copy number calling and SNV classification using targeted short read sequencing
Version 1.6.2

This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.

AuthorMarkus Riester [aut, cre], Angad P. Singh [aut]
Bioconductor views CopyNumberVariation Coverage Sequencing Software VariantAnnotation VariantDetection
Date of publicationNone
MaintainerMarkus Riester <markus.riester@novartis.com>
LicenseArtistic-2.0
Version1.6.2
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PureCN")

Getting started

README.md

Popular man pages

callLOH: Get regions of LOH
correctCoverageBias: Correct for GC bias
getDiploid: Function to extract diploid solutions.
getSexFromCoverage: Get sample sex from coverage
PureCN-defunct: Defunct functions in package 'PureCN'
readCoverageGatk: Read GATK coverage files
segmentationCBS: CBS segmentation
See all...

All man pages Function index File listing

Man pages

autoCurateResults: Heuristics to find the best purity/ploidy solution.
bootstrapResults: Filter unlikely purity/ploidy solutions
calculateBamCoverageByInterval: Function to calculate coverage from BAM file
calculateGCContentByInterval: Calculates GC content by interval
calculateLogRatio: Calculate coverage log-ratio of tumor vs. normal
calculatePowerDetectSomatic: Power calculation for detecting somatic mutations
callAlterations: Calling of amplifications and deletions
callAlterationsFromSegmentation: Calling of amplifications and deletions from segmentations
callLOH: Get regions of LOH
centromeres: A list of data.frames containing centromere positions.
correctCoverageBias: Correct for GC bias
createCurationFile: Create file to curate PureCN results
createExonWeightFile: Calculate exon weights
createNormalDatabase: Create database of normal samples
createSNPBlacklist: Create SNP black list
createTargetWeights: Calculate target weights
filterTargets: Remove low quality targets
filterVcfBasic: Basic VCF filter function
filterVcfMuTect: Filter VCF MuTect
findBestNormal: Find best normal sample in database
findFocal: Find focal amplifications
getDiploid: Function to extract diploid solutions.
getSexFromCoverage: Get sample sex from coverage
getSexFromVcf: Get sample sex from a VCF file
plotAbs: Plots for analyzing PureCN solutions
plotBestNormal: Plot the PCA of tumor and its best normal(s)
poolCoverage: Pool coverage from multiple samples
predictSomatic: Predict germline vs. somatic status
PureCN-defunct: Defunct functions in package 'PureCN'
PureCN-deprecated: Deprecated functions in package 'PureCN'
purecn.example.output: Example output
readCoverageFile: Read coverage file
readCoverageGatk: Read GATK coverage files
readCurationFile: Read curation file
runAbsoluteCN: Run PureCN implementation of ABSOLUTE
segmentationCBS: CBS segmentation
segmentationPSCBS: PSCBS segmentation
setMappingBiasVcf: Set Mapping Bias VCF
setPriorVcf: Set Somatic Prior VCF

Functions

CNV.analyze2 Source code
PSCBSoutput2DNAcopy Source code
PureCN-defunct Man page
PureCN-deprecated Man page
add.chr.name Source code
addADField Source code
addCosmicCNT Source code
addDbField Source code
addDpField Source code
addFaField Source code
addSymbols Source code
addVoomToGeneCalls Source code
annotatePosteriorsVcf Source code
annotateVcfTarget Source code
appendComment Source code
autoCurateResults Man page Source code
bootstrapResults Man page Source code Source code
calcComplexityCopyNumber Source code
calcFractionBalanced Source code
calcGCmetric Source code
calcLlikSegment Source code
calcLlikSegmentClonal Source code
calcLlikSegmentExonLrs Source code
calcLlikSegmentSubClonal Source code
calcMsSegment Source code
calcMsSegmentC Source code
calcPuritySomaticVariants Source code
calcSNVLLik Source code
calcTargetedGenome Source code
calculateBamCoverageByInterval Man page Source code
calculateGCContentByInterval Man page Source code
calculateLogRatio Man page Source code
calculatePowerDetectSomatic Man page Source code
callAlterations Man page Source code
callAlterationsFromSegmentation Man page Source code
callLOH Man page Source code
centromeres Man page
checkArgs Source code
checkFraction Source code
checkGCBias Source code
checkIntervals Source code
checkLowCoverage Source code
checkNormalDB Source code
checkParameters Source code
checkSeg Source code
checkSymbolsChromosome Source code
checkVcfFieldAvailable Source code
cleanupSample Source code
correctCoverageBias Man page Source code
correctCoverageBiasLoess Source code
correctCoverageBiasPolynomial Source code
createCurationFile Man page Source code
createExonWeightFile Man page Source code
createFakeLogRatios Source code
createNormalDatabase Man page Source code
createSNPBlacklist Man page Source code
createTargetWeights Man page Source code
extractMLSNVState Source code
failedNonAberrant Source code
filterDuplicatedCandidates Source code
filterDuplicatedResults Source code
filterTargets Man page Source code
filterTargetsChrHash Source code
filterTargetsCoverage Source code
filterTargetsLowHighGC Source code
filterTargetsNormalDB Source code
filterTargetsTargetedBase Source code
filterVcfBasic Man page Source code
filterVcfMuTect Man page Source code
findBestNormal Man page Source code
findCNNLOH Source code
findFocal Man page Source code
findLocalMinima Source code
fixAllosomeCoverage Source code
fixAllosomeSegmentation Source code
flagBootstrap Source code
flagResult Source code
flagResults Source code
gcGeneToCoverage Source code
gcPos Source code
get2DPurityGrid Source code
getAFPlotGroups Source code
getArmLocations Source code
getCentromerePositions Source code
getChrHash Source code
getDiploid Man page Source code
getFractionLoh Source code
getGeneCalls Source code
getGoF Source code
getMajorityStateTargets Source code
getNormalIdInVcf Source code
getPruneH Source code
getSDundo Source code
getSegSizes Source code
getSex Source code
getSexChr Source code
getSexFromCoverage Man page Source code
getSexFromRds Source code
getSexFromVcf Man page Source code
getTumorIdInVcf Source code
getVariantPosteriors Source code
legend.col Source code
loadGcGeneFile Source code
loadSegFile Source code
logFooter Source code
logHeader Source code
matrixTotalPloidyToTumorPloidy Source code
nferPloidyRegions Source code
normalizeRunningMedian Source code
optimizeGrid Source code
plotAbs Man page Source code
plotBestNormal Man page Source code
plotContamination Source code
plotVolcano Source code
poolCoverage Man page Source code
postprocessLogRatios Source code
predictSomatic Man page Source code
pruneByHclust Source code
pruneByVCF Source code
purecn.example.output Man page
rankResults Source code
readAndCheckVcf Source code
readCoverageFile Man page Source code
readCoverageGatk Man page Source code Source code
readCurationFile Man page Source code
readNormalPanelVcfLarge Source code
readNormals Source code
removeChr Source code
removeOutliers Source code
runAbsoluteCN Man page Source code
sampleOffset Source code
sampleOffsetFast Source code
segmentationCBS Man page Source code
segmentationPSCBS Man page Source code
setMappingBiasVcf Man page Source code
setPriorVcf Man page Source code
smoothVectorByChromosome Source code
stopRuntimeError Source code
stopUserError Source code
strip.chr.name Source code
testGermline Source code
toLines Source code
updateNumMark Source code
voomCountMatrix Source code
voomLogRatio Source code
voomTargets Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/PureCN-internal.R
R/bootstrapResults.R
R/calculateBamCoverageByInterval.R
R/calculateGCContentByInterval.R
R/calculateLogRatio.R
R/callAlterations.R
R/callLOH.R
R/correctCoverageBias.R
R/createCurationFile.R
R/createNormalDatabase.R
R/createSNPBlacklist.R
R/curateResults.R
R/filterTargets.R
R/filterVcf.R
R/findBestNormal.R
R/findFocal.R
R/getSex.R
R/plotAbs.R
R/poolCoverage.R
R/powerDetectSomatic.R
R/predictSomatic.R
R/readCoverageFile.R
R/readCurationFile.R
R/runAbsoluteCN.R
R/segmentationCBS.R
R/segmentationPSCBS.R
R/setMappingBiasVcf.R
README.md
build
build/vignette.rds
data
data/centromeres.rda
data/purecn.example.output.rda
inst
inst/CITATION
inst/doc
inst/doc/PureCN.R
inst/doc/PureCN.Rnw
inst/doc/PureCN.pdf
inst/doc/Quick.R
inst/doc/Quick.Rnw
inst/doc/Quick.pdf
inst/extdata
inst/extdata/Coverage.R
inst/extdata/IntervalFile.R
inst/extdata/NormalDB.R
inst/extdata/PureCN.R
inst/extdata/downloadCentromeres.R
inst/extdata/ex1.bam
inst/extdata/ex1.bam.bai
inst/extdata/ex1_gcgene.txt
inst/extdata/ex1_intervals.txt
inst/extdata/ex2_intervals.bed
inst/extdata/ex2_intervals.txt
inst/extdata/ex2_reference.fa
inst/extdata/ex2_reference.fa.fai
inst/extdata/example_cosmic.vcf.gz
inst/extdata/example_cosmic.vcf.gz.tbi
inst/extdata/example_gc.gene.file.txt
inst/extdata/example_normal.list
inst/extdata/example_normal.txt
inst/extdata/example_normal2.txt
inst/extdata/example_seg.txt
inst/extdata/example_tumor.txt
inst/extdata/example_vcf.vcf
inst/extdata/test_coverage_overlapping_intervals.txt
inst/unitTests
inst/unitTests/test_autoCurateResults.R
inst/unitTests/test_bootstrapResults.R
inst/unitTests/test_calculateBamCoverageByInterval.R
inst/unitTests/test_calculateGCContentByInterval.R
inst/unitTests/test_calculatePowerDetectSomatic.R
inst/unitTests/test_callAlterations.R
inst/unitTests/test_callAlterationsFromSegmentation.R
inst/unitTests/test_callLOH.R
inst/unitTests/test_correctCoverageBias.R
inst/unitTests/test_createCurationFile.R
inst/unitTests/test_createNormalDatabase.R
inst/unitTests/test_filterVcf.R
inst/unitTests/test_findFocal.R
inst/unitTests/test_getDiploid.R
inst/unitTests/test_getSexFromCoverage.R
inst/unitTests/test_getSexFromVcf.R
inst/unitTests/test_poolCoverage.R
inst/unitTests/test_predictSomatic.R
inst/unitTests/test_readCoverageFile.R
inst/unitTests/test_runAbsoluteCN.R
inst/unitTests/test_setMappingBiasVcf.R
inst/unitTests/test_setPriorVcf.R
man
man/PureCN-defunct.Rd
man/PureCN-deprecated.Rd
man/autoCurateResults.Rd
man/bootstrapResults.Rd
man/calculateBamCoverageByInterval.Rd
man/calculateGCContentByInterval.Rd
man/calculateLogRatio.Rd
man/calculatePowerDetectSomatic.Rd
man/callAlterations.Rd
man/callAlterationsFromSegmentation.Rd
man/callLOH.Rd
man/centromeres.Rd
man/correctCoverageBias.Rd
man/createCurationFile.Rd
man/createExonWeightFile.Rd
man/createNormalDatabase.Rd
man/createSNPBlacklist.Rd
man/createTargetWeights.Rd
man/filterTargets.Rd
man/filterVcfBasic.Rd
man/filterVcfMuTect.Rd
man/findBestNormal.Rd
man/findFocal.Rd
man/getDiploid.Rd
man/getSexFromCoverage.Rd
man/getSexFromVcf.Rd
man/plotAbs.Rd
man/plotBestNormal.Rd
man/poolCoverage.Rd
man/predictSomatic.Rd
man/purecn.example.output.Rd
man/readCoverageFile.Rd
man/readCoverageGatk.Rd
man/readCurationFile.Rd
man/runAbsoluteCN.Rd
man/segmentationCBS.Rd
man/segmentationPSCBS.Rd
man/setMappingBiasVcf.Rd
man/setPriorVcf.Rd
tests
tests/runTests.R
vignettes
vignettes/PureCN.Rnw
vignettes/PureCN.bib
vignettes/Quick.Rnw
PureCN documentation built on May 25, 2017, 2:03 a.m.

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