Copy number calling and SNV classification using targeted short read sequencing

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Documentation for package ‘PureCN’ version 2.15.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

adjustLogRatio	Adjust tumor vs. normal coverage log ratio for tumor purity and ploidy
annotateTargets	Annotate targets with gene symbols
bootstrapResults	Bootstrapping variant fits
calculateBamCoverageByInterval	Function to calculate coverage from BAM file
calculateLogRatio	Calculate coverage log-ratio of tumor vs. normal
calculateMappingBiasGatk4	Calculate Mapping Bias from GATK4 GenomicsDB
calculateMappingBiasVcf	Calculate Mapping Bias
calculatePowerDetectSomatic	Power calculation for detecting somatic mutations
calculateTangentNormal	Calculate tangent normal
callAlterations	Calling of amplifications and deletions
callAlterationsFromSegmentation	Calling of amplifications and deletions from segmentations
callAmplificationsInLowPurity	Calling of amplifications in low purity samples
callCIN	Call Chromosomal Instability
callLOH	Get regions of LOH
callMutationBurden	Call mutation burden
centromeres	A list of data.frames containing centromere positions.
correctCoverageBias	Correct for library-specific coverage biases
createCurationFile	Create file to curate PureCN results
createNormalDatabase	Create database of normal samples
filterIntervals	Remove low quality intervals
filterVcfBasic	Basic VCF filter function
filterVcfMuTect	Filter VCF MuTect
filterVcfMuTect2	Filter VCF MuTect2
findFocal	Find focal amplifications
findHighQualitySNPs	Find High Quality SNPs
getSexFromCoverage	Get sample sex from coverage
getSexFromVcf	Get sample sex from a VCF file
plotAbs	Plots for analyzing PureCN solutions
poolCoverage	Pool coverage from multiple samples
predictSomatic	Predict germline vs. somatic status
preprocessIntervals	Preprocess intervals
processMultipleSamples	Multi sample normalization and segmentation
PureCN-defunct	Defunct functions in package 'PureCN'
PureCN-deprecated	Deprecated functions in package 'PureCN'
purecn.DNAcopy.bdry	DNAcopy boundary data
purecn.example.output	Example output
readAllelicCountsFile	Read allelic counts file
readCoverageFile	Read coverage file
readCurationFile	Read curation file
readIntervalFile	Read interval file
readLogRatioFile	Read file containing interval-level log2 tumor/normal ratios
readSegmentationFile	Read file containing segmentations
runAbsoluteCN	Run PureCN implementation of ABSOLUTE
segmentationCBS	CBS segmentation
segmentationGATK4	GATK4 ModelSegments segmentation function
segmentationHclust	Minimal segmentation function
segmentationPSCBS	PSCBS segmentation
setMappingBiasVcf	Set Mapping Bias VCF
setPriorVcf	Set Somatic Prior VCF