| 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-defunct | Defunct functions in package 'PureCN' |
| PureCN-deprecated | Deprecated functions in package 'PureCN' |
| purecn.example.output | Example output |
| readCoverageFile | Read coverage file |
| 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 |