API for TitanCNA
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
| Global functions | |
|---|---|
| .onLoad | Source code |
| EMresults | Man page |
| TitanCNA | Man page |
| TitanCNA-dataset | Man page |
| TitanCNA-package | Man page |
| allelicRatioBasedCN | Source code |
| 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 |
| 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 |
| 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 |
| plotClonalFrequency | Man page Source code |
| plotHaplotypeFraction | Man page 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 |
| wigToGRanges | Man page Source code |
| wigToRangedData | Man page Source code |
