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

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PureCN")
AuthorMarkus Riester
Bioconductor views CopyNumberVariation Coverage Sequencing Software VariantAnnotation VariantDetection
Date of publicationNone
MaintainerMarkus Riester <markus.riester@novartis.com>
LicenseArtistic-2.0
Version1.2.3

View on Bioconductor

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-deprecated: Deprecated functions in package 'PureCN'

purecn.example.output: Example output

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

autoCurateResults Man page
bootstrapResults Man page
calculateBamCoverageByInterval Man page
calculateGCContentByInterval Man page
calculateLogRatio Man page
calculatePowerDetectSomatic Man page
callAlterations Man page
callAlterationsFromSegmentation Man page
callLOH Man page
centromeres Man page
correctCoverageBias Man page
createCurationFile Man page
createExonWeightFile Man page
createNormalDatabase Man page
createSNPBlacklist Man page
createTargetWeights Man page
filterTargets Man page
filterVcfBasic Man page
filterVcfMuTect Man page
findBestNormal Man page
findFocal Man page
getDiploid Man page
getSexFromCoverage Man page
getSexFromVcf Man page
plotAbs Man page
plotBestNormal Man page
poolCoverage Man page
predictSomatic Man page
PureCN-deprecated Man page
purecn.example.output Man page
readCoverageGatk Man page
readCurationFile Man page
runAbsoluteCN Man page
segmentationCBS Man page
segmentationPSCBS Man page
setMappingBiasVcf Man page
setPriorVcf Man page

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/readCoverageGatk.R R/readCurationFile.R R/runAbsoluteCN.R R/segmentationCBS.R R/segmentationPSCBS.R R/setMappingBiasVcf.R
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/extdata
inst/extdata/Coverage.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_intervals.txt
inst/extdata/ex2_intervals.txt
inst/extdata/ex2_reference.fa
inst/extdata/example_cosmic.vcf.gz
inst/extdata/example_cosmic.vcf.gz.tbi
inst/extdata/example_gc.gene.file.txt
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_createSNPBlacklist.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_readCoverageGatk.R inst/unitTests/test_runAbsoluteCN.R inst/unitTests/test_setMappingBiasVcf.R inst/unitTests/test_setPriorVcf.R
man
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/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

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