API for afrangou/CleanCNA
Calling and recalling subclonal copy number using SNP and SNV information to provide a high quality set of copy number profiles.

Global functions
AssessBBDPCRun Man page Source code
AssessBBDPCRun_B Man page Source code
AssessBBDPCRun_afterpeakcalling Man page Source code
CNAsDriversComplexHeatmap Man page Source code
CNAsDriversHeatmapDendrogram Man page Source code
CleanBedopsOutput Man page Source code
CodeSegments Man page Source code
CodeSegments_test Man page Source code
CollateSubclones Man page Source code
ComputePeaksVAF Man page Source code
ComputePeaksVAF_nf Man page Source code
ConvertImputeInputToBeagleInput.Rd Man page
ConvertSubclones Source code
ConvertSubclonesSingleSample Man page
CreateScriptsDirs Man page Man page Source code
CreateScriptsDirsBeagle Man page
CreateScriptsDirsFixedParams Man page Source code
CreateWGDScriptDirs Man page
CreateWGDrun Source code
GenerateDPinput Man page Source code Source code
GenerateDPinput_mutect_vcf Man page Source code
GenerateDPinput_strelka_vcf Man page Source code
GenerateDPinput_t2BamAC Man page Man page
GenerateDPinputt2BamAC Source code
GenerateDPinputt2BamAC_Beagle Source code
GenerateDPinputt2BamAC_Beagle_nf Man page Man page Source code
GenomewideStackedBar Man page Source code
GenomewideStackedBarPlot Man page Source code
LabelGenomecov Man page Source code
PassFail Man page Source code
PrepDataForSummary Man page
PrepShapeIt2 Man page Source code
QualityControl_CNAqc Man page
RunBeagle5 Man page
RunDPClust Man page Source code
RunDPClust_Beagle_nf Man page Source code
RunShapeIt2 Man page
SetUpRun2BBDPC Man page Source code
WriteBeagleAsImpute Man page
call.peaks Man page Source code
compute.expected.peak.loc Man page
computed.expected.peak.loc Source code
convert.impute.input.to.beagle.input Source code
estimate.dpclust.purity Source code Source code
estimate.new.ploidy Source code Source code
get.worst.filter Source code Source code
larger.all.later.numbers Source code Source code
log.message Source code Source code
pastedot Source code Source code
pasteu Source code Source code
prepDataForSummary Man page Source code
qc Source code
qc_CNAqc Source code
read.segs Man page Source code
read.snvs Man page Source code
reestimate.purity Man page Source code
run.beagle5 Source code
switch.ploidy.get.ploidy Source code Source code
switch.ploidy.get.purity Source code Source code
writebeagle.as.impute Source code
afrangou/CleanCNA documentation built on Dec. 28, 2021, 8:21 p.m.