Copy number calling and SNV classification using targeted short read sequencing


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Documentation for package ‘PureCN’ version 1.2.3

Help 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