PureCN-deprecated       Deprecated functions in package 'PureCN'
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.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
