Files in PureCN

Copy number calling and SNV classification using targeted short read sequencing

README.md R/readSegmentationFile.R R/PureCN-internal.R R/poolCoverage.R R/filterVcfMuTect.R R/calculateIntervalWeights.R R/readCoverageFile.R R/bootstrapResults.R R/powerDetectSomatic.R R/processMultipleSamples.R R/segmentationHclust.R R/callMutationBurden.R R/filterIntervals.R R/correctCoverageBias.R R/setMappingBiasVcf.R R/calculateLogRatio.R R/runAbsoluteCN.R R/filterVcfMuTect2.R R/plotAbs.R R/segmentationPSCBS.R R/createNormalDatabase.R R/getSex.R R/readCurationFile.R R/findFocal.R R/callAmplificationsInLowPurity.R R/readLogRatioFile.R R/calculateBamCoverageByInterval.R R/preprocessIntervals.R R/predictSomatic.R R/filterVcf.R R/annotateTargets.R R/calculateMappingBiasVcf.R R/callLOH.R R/createCurationFile.R R/callAlterations.R R/setPriorVcf.R R/segmentationCBS.R R/callCIN.R vignettes/Quick.Rmd man/callMutationBurden.Rd man/readCurationFile.Rd man/calculateTangentNormal.Rd man/PureCN-defunct.Rd man/calculatePowerDetectSomatic.Rd man/findFocal.Rd man/calculateMappingBiasGatk4.Rd man/segmentationPSCBS.Rd man/calculateLogRatio.Rd man/setMappingBiasVcf.Rd man/calculateBamCoverageByInterval.Rd man/createCurationFile.Rd man/purecn.example.output.Rd man/PureCN-deprecated.Rd man/plotAbs.Rd man/calculateIntervalWeights.Rd man/filterVcfMuTect.Rd man/getSexFromVcf.Rd man/callAmplificationsInLowPurity.Rd man/annotateTargets.Rd man/getSexFromCoverage.Rd man/createNormalDatabase.Rd man/readLogRatioFile.Rd man/bootstrapResults.Rd man/predictSomatic.Rd man/setPriorVcf.Rd man/segmentationCBS.Rd man/correctCoverageBias.Rd man/readCoverageFile.Rd man/callAlterationsFromSegmentation.Rd man/readSegmentationFile.Rd man/purecn.DNAcopy.bdry.Rd man/callAlterations.Rd man/segmentationHclust.Rd man/preprocessIntervals.Rd man/runAbsoluteCN.Rd man/poolCoverage.Rd man/processMultipleSamples.Rd man/callLOH.Rd man/calculateMappingBiasVcf.Rd man/filterVcfMuTect2.Rd man/callCIN.Rd man/filterIntervals.Rd man/filterVcfBasic.Rd man/centromeres.Rd tests/testthat.R tests/testthat/test_setPriorVcf.R tests/testthat/test_callMutationBurden.R tests/testthat/test_callCIN.R tests/testthat/test_readCoverageFile.R tests/testthat/test_plotAbs.R tests/testthat/test_callAlterationsFromSegmentation.R tests/testthat/test_correctCoverageBias.R tests/testthat/test_createCurationFile.R tests/testthat/test_readSegmentationFile.R tests/testthat/test_setMappingBiasVcf.R tests/testthat/test_getSexFromCoverage.R tests/testthat/test_predictSomatic.R tests/testthat/test_bootstrapResults.R tests/testthat/test_processMultipleSamples.R tests/testthat/test_callAmplificationsInLowPurity.R tests/testthat/test_runAbsoluteCN.R tests/testthat/test_createNormalDatabase.R tests/testthat/test_calculatePowerDetectSomatic.R tests/testthat/test_callLOH.R tests/testthat/test_preprocessIntervals.R tests/testthat/test_getSexFromVcf.R tests/testthat/test_poolCoverage.R tests/testthat/test_readLogRatioFile.R tests/testthat/test_calculateBamCoverageByInterval.R tests/testthat/test_callAlterations.R tests/testthat/test_segmentation.R tests/testthat/test_findFocal.R tests/testthat/test_filterVcf.R tests/testthat/test_annotateTargets.R inst/doc/Quick.Rmd inst/doc/PureCN.pdf inst/doc/Quick.R inst/doc/PureCN.R inst/extdata/FilterCallableLoci.R inst/extdata/BenchmarkTumorOnly.R inst/extdata/Dx.R inst/extdata/NormalDB.R inst/extdata/PureCN.R inst/extdata/IntervalFile.R inst/extdata/Coverage.R inst/extdata/dist/calculateSbdry.R inst/extdata/dist/downloadCentromeres.R