Estimating tumor purity, ploidy, LOH, and SNV status using hybrid capture NGS data


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Documentation for package ‘PureCN’ version 1.0.4

Help Pages

chr.hash A data.frame of chromosome names.
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
filterVcfBasic Basic VCF filter function
filterVcfMuTect Filter VCF MuTect
findBestNormal Find best normal sample in database
findFocal Find focal amplifications
getSexFromCoverage Get sample sex from coverage
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.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
setPriorVcf Set Somatic Prior VCF