API for lima1/PureCN
Copy number calling and SNV classification using targeted short read sequencing
| Global functions | |
|---|---|
| .CNV.analyze2 | Source code |
| .MoM | Source code |
| .PSCBSgetKnownSegments | Source code |
| .PSCBSinput | Source code |
| .PSCBSoutput2DNAcopy | Source code |
| .add.chr.name | Source code |
| .addADField | Source code |
| .addAverageCoverage | Source code |
| .addAverageWeights | Source code |
| .addBqField | Source code |
| .addCosmicCNT | Source code |
| .addDbField | Source code |
| .addDpField | Source code |
| .addFaField | Source code |
| .addFilterFlag | Source code |
| .addGCData | Source code |
| .addScoreToGr | Source code |
| .addSomaticField | Source code |
| .addSymbols | Source code |
| .add_allelic_imbalance | Source code |
| .adjustEmpBayes | Source code |
| .annotateIntervalsGC | Source code |
| .annotateIntervalsMappability | Source code |
| .annotateIntervalsOfftarget | Source code |
| .annotateIntervalsReptiming | Source code |
| .annotateMappingBias | Source code |
| .annotateMappingBiasVcf | Source code |
| .annotatePosteriorsVcf | Source code |
| .annotateVcfPrior | Source code |
| .annotateVcfTarget | Source code |
| .appendComment | Source code |
| .bootstrapResults | Source code |
| .calcComplexityCopyNumber | Source code |
| .calcExpectedRatio | Source code |
| .calcFractionBalanced | Source code |
| .calcGCmetric | Source code |
| .calcIdealPeaks | Source code |
| .calcLlikSegment | Source code |
| .calcLlikSegmentClonal | Source code |
| .calcLlikSegmentExonLrs | Source code |
| .calcLlikSegmentSubClonal | Source code |
| .calcMinSupportingReadsForFiltering | Source code |
| .calcMinSupportingReadsForPower | Source code |
| .calcMsSegment | Source code |
| .calcMsSegmentC | Source code |
| .calcMultisamplePosteriors | Source code |
| .calcPuritySomaticVariants | Source code |
| .calcSNVLLik | Source code |
| .calcTargetedGenome | Source code |
| .calculateIntervalWeights | Source code |
| .calculateMappingBias | Source code |
| .calculate_allelic_imbalance | Source code |
| .calculate_ccf | Source code |
| .calculate_tumor_normal_noise_ratio | Source code |
| .calibrate_log_ratio | Source code |
| .calibrate_off_target_log_ratio | Source code |
| .checkADField | Source code |
| .checkArgs | Source code |
| .checkColScore | Source code |
| .checkFraction | Source code |
| .checkGATK4Version | Source code |
| .checkGCBias | Source code |
| .checkIntervals | Source code |
| .checkLowCoverage | Source code |
| .checkNormalDB | Source code |
| .checkParameters | Source code |
| .checkParametersSegmentation | Source code |
| .checkSeg | Source code |
| .checkSegFormatting | Source code |
| .checkSeqlengths | Source code |
| .checkSeqlevelStyle | Source code |
| .checkSymbolsChromosome | Source code |
| .checkTargetWidth | Source code |
| .checkVcfFieldAvailable | Source code |
| .checkVcfNotEmpty | Source code |
| .clusterFa | Source code |
| .convertSegGATK4 | Source code |
| .correctCoverageBiasLoess | Source code |
| .correctRepTimingBiasLinear | Source code |
| .countVariants | Source code |
| .coverageHasCounts | Source code |
| .createCoverageGgplot | Source code |
| .createFakeLogRatios | Source code |
| .debugSegmentation | Source code |
| .denoiseSample | Source code |
| .detectCaller | Source code |
| .dropShortUntargetedSeqLevels | Source code |
| .estimateCallableRegions | Source code |
| .estimateContamination | Source code |
| .excludeIntervals | Source code |
| .extractCountMatrix | Source code |
| .extractMLSNVState | Source code |
| .failedNonAberrant | Source code |
| .filterDuplicatedCandidates | Source code |
| .filterDuplicatedResults | Source code |
| .filterDuplicates | Source code |
| .filterIntervalsCentromeres | Source code |
| .filterIntervalsChrHash | Source code |
| .filterIntervalsCoverage | Source code |
| .filterIntervalsCreateNormalDB | Source code |
| .filterIntervalsLowHighGC | Source code |
| .filterIntervalsMappability | Source code |
| .filterIntervalsNormalDB | Source code |
| .filterIntervalsNotNA | Source code |
| .filterIntervalsOfftarget | Source code |
| .filterIntervalsTargetedBase | Source code |
| .filterIntervalsTotalCounts | Source code |
| .filterIntervalsTotalNormalCoverage | Source code |
| .filterVcfByBQ | Source code |
| .findCNNLOH | Source code |
| .findClosestSolution | Source code |
| .findLocalMinima | Source code |
| .findOverlapsCheckAlt | Source code |
| .fixAllosomeCoverage | Source code |
| .fixAllosomeSegmentation | Source code |
| .fixBreakpointsInBaits | Source code |
| .fixStartEndPos | Source code |
| .flagBootstrap | Source code |
| .flagResult | Source code |
| .flagResults | Source code |
| .gcGeneToCoverage | Source code |
| .get2DPurityGrid | Source code |
| .getAFPlotGroups | Source code |
| .getArmLocations | Source code |
| .getAverageWeightPV | Source code |
| .getBQFromVcf | Source code |
| .getCNAobject | Source code |
| .getCentromerePositions | Source code |
| .getCentromeres | Source code |
| .getChrHash | Source code |
| .getColScore | Source code |
| .getExonLrs | Source code |
| .getFormat | Source code |
| .getFractionLoh | Source code |
| .getGeneCalls | Source code |
| .getGoF | Source code |
| .getLogRatioFormat | Source code |
| .getNormalIdInVcf | Source code |
| .getPruneH | Source code |
| .getPureCNPrefixVcf | Source code |
| .getSDundo | Source code |
| .getSampleIdFromVcf | Source code |
| .getSegFormat | Source code |
| .getSegSizes | Source code |
| .getSeqlevelsStyle | Source code |
| .getSex | Source code |
| .getSexChr | Source code |
| .getSexFromRds | Source code |
| .getSizeDomState | Source code |
| .getTumorIdInVcf | Source code |
| .getVariantPosteriors | Source code |
| .imputeBetaBin | Source code |
| .isFakeLogRatio | Source code |
| .isRareKaryotype | Source code |
| .legend.col | Source code |
| .logFooter | Source code |
| .logHeader | Source code |
| .matrixTotalPloidyToTumorPloidy | Source code |
| .optimizeGrid | Source code |
| .padGranges | Source code |
| .parseADGenomicsDb | Source code |
| .parseGATKHeader | Source code |
| .plotGcBias | Source code |
| .plotIntervalWeights | Source code |
| .plotLogRatios | Source code |
| .plotRepBias | Source code |
| .plotTypeAF | Source code |
| .plotTypeBAF | Source code |
| .plotTypeHist | Source code |
| .plotTypeOverview | Source code |
| .postprocessLogRatios | Source code |
| .pruneByHclust | Source code |
| .pruneByVCF | Source code |
| .rankResults | Source code |
| .readAllelicCountsFileGatk4 | Source code |
| .readAndCheckVcf | Source code |
| .readCoverageCnn | Source code |
| .readCoverageGatk3 | Source code |
| .readCoverageGatk4 | Source code |
| .readLogRatioFileGATK3 | Source code |
| .readLogRatioFileGATK4 | Source code |
| .readNormalPanelVcfLarge | Source code |
| .readNormals | Source code |
| .remove0MappabilityRegions | Source code |
| .removeChr | Source code |
| .removeOutliers | Source code |
| .removeVariants | Source code |
| .robustSd | Source code |
| .sampleError | Source code |
| .sampleOffset | Source code |
| .sampleOffsetFast | Source code |
| .splitIntervals | Source code |
| .standardizeNormals | Source code |
| .stopRuntimeError | Source code |
| .stopUserError | Source code |
| .strip.chr.name | Source code |
| .testGermline | Source code |
| .tileReptiming | Source code |
| .toLines | Source code |
| .updateNumMark | Source code |
| .warnLowCoverageTargets | Source code |
| .writeAllelicCountsFileGatk | Source code |
| .writeCoverage | Source code |
| .writeGATKHeader | Source code |
| .writeIntervals | Source code |
| .writeLogRatioFileGATK4 | Source code |
| .writeQCFile | Source code |
| PureCN-defunct | Man page |
| PureCN-deprecated | Man page |
| annotateTargets | Man page Source code |
| bootstrapResults | Man page Source code |
| calculateBamCoverageByInterval | Man page Source code |
| calculateLogRatio | Man page Source code |
| calculateMappingBiasGatk4 | Man page Source code |
| calculateMappingBiasVcf | Man page Source code |
| calculatePowerDetectSomatic | Man page Source code |
| calculateTangentNormal | Man page Source code |
| callAlterations | Man page Source code |
| callAlterationsFromSegmentation | Man page Source code |
| callAmplificationsInLowPurity | Man page Source code |
| callCIN | Man page Source code |
| callLOH | Man page Source code |
| callMutationBurden | Man page Source code |
| centromeres | Man page |
| correctCoverageBias | Man page Source code |
| createCurationFile | Man page Source code |
| createNormalDatabase | Man page Source code |
| filterIntervals | Man page Source code |
| filterVcfBasic | Man page Source code |
| filterVcfMuTect | Man page Source code |
| filterVcfMuTect2 | Man page Source code |
| findFocal | Man page Source code |
| getSexFromCoverage | Man page Source code |
| getSexFromVcf | Man page Source code |
| plotAbs | Man page Source code |
| poolCoverage | Man page Source code |
| predictSomatic | Man page Source code |
| preprocessIntervals | Man page Source code |
| processMultipleSamples | Man page Source code |
| purecn.DNAcopy.bdry | Man page |
| purecn.example.output | Man page |
| readAllelicCountsFile | Man page Source code |
| readCoverageFile | Man page Source code |
| readCurationFile | Man page Source code |
| readIntervalFile | Man page Source code |
| readLogRatioFile | Man page Source code |
| readSegmentationFile | Man page Source code |
| runAbsoluteCN | Man page Source code |
| segmentationCBS | Man page Source code |
| segmentationGATK4 | Man page Source code |
| segmentationHclust | Man page Source code |
| segmentationPSCBS | Man page Source code |
| setMappingBiasVcf | Man page Source code |
| setPriorVcf | Man page Source code |
