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.

AuthorMarkus Riester
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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.