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 |