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 |