API for gavinha/TitanCNA
Subclonal copy number and LOH prediction from whole genome sequencing of tumours

Global functions
EMresults Man page
TitanCNA Man page
TitanCNA-dataset Man page
TitanCNA-package Man page
asCovarianceMatrix Source code
betabinomialpdflog Source code
betapdflog Source code
binomialpdflog Source code
bivariateNormalpdflog Source code
clonalCNDerivativeNUpdateEqn Source code
clonalCNDerivativePloidyUpdateEqn Source code
clonalCNDerivativeSUpdateEqn Source code
clonalCNDerivativeVarExactUpdateEqn Source code
clonalCNDerivativeVarUpdateEqn Source code
clonalTwoComponentMixtureCN Source code
computeBIC Source code
computeBinomialObslik Source code
computeBivariateNormalObslik Source code
computeNormalObslik Source code
computeSDbwIndex Man page Source code
convergeParams Man page
correctIntegerCN Man page Source code
correctReadDepth Man page Source code
correctReadcount Source code
covarLikelihoodFun Source code
data Man page
decodeLOH Source code
decoupleMegaVar Source code
dirichletpdflog Source code
estimateBetaParamsMap Source code
estimateClonalCNParamsMap Source code
estimateClonalMixWeightsParamMap Source code
estimateDirichletParamsMap Source code
estimateGenotypeMixWeightsParamMap Source code
estimateInvGammaParamsMap Source code
excludeGarbageState Source code
extendSegments Source code
extractAlleleReadCounts Source code
filterData Man page Source code
getBivariateCovariance Source code
getGenomeWidePositions Source code
getHaplotypesFromVCF Man page Source code
getMajorMinorCN Source code
getOverlap Source code
getPhasedAllele Source code
getPhasedAlleleFraction Source code
getPositionOverlap Man page Source code
getSubcloneProfiles Source code
invWishartpdflog Source code
invgammapdflog Source code
keepChr Source code
likelihoodFunc Source code
loadAlleleCounts Man page Source code
loadBXcountsFromBEDDir Man page Source code
loadDefaultParameters Man page Source code
loadHaplotypeAlleleCounts Man page Source code
loadReadCountsFromBed Source code
logRbasedCN Source code
mergeSegsByCol Source code
multiGammaFunlog Source code
normalpdflog Source code
onLoad Source code
outlierObslik Source code
outputModelParameters Man page Source code
outputTitanResults Man page Source code
outputTitanSegments Man page Source code
plotAllelicCN Source code
plotAllelicRatio Man page Source code
plotCNlogRByChr Man page Source code
plotChrLines Source code
plotClonalFrequency Man page Source code
plotGeneAnnotation Source code
plotHaplotypeFraction Man page Source code
plotIdiogram.hg38 Source code
plotSegmentMedians Man page Source code
plotSubcloneProfiles Man page Source code
printSDbw Source code
priorProbs Source code
removeCentromere Source code
removeCentromereSegs Source code
removeEmptyClusters Source code
runEMclonalCN Man page Source code
sdbw.density Source code
setGenomeStyle Man page Source code
setupClonalParameters Source code
updateParameters Source code
viterbiClonalCN Man page Source code
wigToRangedData Man page Source code
gavinha/TitanCNA documentation built on Dec. 8, 2018, 11:22 p.m.