Man pages for PureCN
Copy number calling and SNV classification using targeted short read sequencing

annotateTargetsAnnotate targets with gene symbols
bootstrapResultsBootstrapping variant fits
calculateBamCoverageByIntervalFunction to calculate coverage from BAM file
calculateGCContentByIntervalCalculates GC content by interval
calculateIntervalWeightsCalculate interval weights
calculateLogRatioCalculate coverage log-ratio of tumor vs. normal
calculateMappingBiasVcfCalculate Mapping Bias
calculatePowerDetectSomaticPower calculation for detecting somatic mutations
calculateTangentNormalCalculate tangent normal
callAlterationsCalling of amplifications and deletions
callAlterationsFromSegmentationCalling of amplifications and deletions from segmentations
callAmplificationsInLowPurityCalling of amplifications in low purity samples
callCINCall Chromosomal Instability
callLOHGet regions of LOH
callMutationBurdenCall mutation burden
centromeresA list of data.frames containing centromere positions.
correctCoverageBiasCorrect for library-specific coverage biases
createCurationFileCreate file to curate PureCN results
createNormalDatabaseCreate database of normal samples
createTargetWeightsCalculate target weights
filterIntervalsRemove low quality intervals
filterTargetsRemove low quality targets
filterVcfBasicBasic VCF filter function
filterVcfMuTectFilter VCF MuTect
filterVcfMuTect2Filter VCF MuTect2
findFocalFind focal amplifications
getSexFromCoverageGet sample sex from coverage
getSexFromVcfGet sample sex from a VCF file
plotAbsPlots for analyzing PureCN solutions
poolCoveragePool coverage from multiple samples
predictSomaticPredict germline vs. somatic status
preprocessIntervalsPreprocess intervals
processMultipleSamplesMulti sample normalization and segmentation
PureCN-defunctDefunct functions in package 'PureCN'
PureCN-deprecatedDeprecated functions in package 'PureCN'
purecn.DNAcopy.bdryDNAcopy boundary data
purecn.example.outputExample output
readCoverageFileRead coverage file
readCurationFileRead curation file
readLogRatioFileRead file containing interval-level log2 tumor/normal ratios
readSegmentationFileRead file containing segmentations
runAbsoluteCNRun PureCN implementation of ABSOLUTE
segmentationCBSCBS segmentation
segmentationHclustMinimal segmentation function
segmentationPSCBSPSCBS segmentation
setMappingBiasVcfSet Mapping Bias VCF
setPriorVcfSet Somatic Prior VCF
PureCN documentation built on Oct. 31, 2019, 2:13 a.m.