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.

Author
Markus Riester
Date of publication
None
Maintainer
Markus Riester <markus.riester@novartis.com>
License
Artistic-2.0
Version
1.2.3

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

Files in this package

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