PureCN-defunct          Defunct functions in package 'PureCN'
PureCN-deprecated       Deprecated functions in package 'PureCN'
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
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.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
