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
calculateGCContentByInterval
                        Calculates GC content by interval
calculateLogRatio       Calculate coverage log-ratio of tumor vs.
                        normal
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
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
createTargetWeights     Calculate target weights
filterTargets           Remove low quality targets
filterVcfBasic          Basic VCF filter function
filterVcfMuTect         Filter VCF MuTect
filterVcfMuTect2        Filter VCF MuTect2
findBestNormal          Find best normal sample in database
findFocal               Find focal amplifications
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
preprocessIntervals     Preprocess intervals
purecn.DNAcopy.bdry     DNAcopy boundary data
purecn.example.output   Example output
readCoverageFile        Read coverage file
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
