API for rmpiro/decompTumor2Sig
Decomposition of individual tumors into mutational signatures by signature refitting
| Global functions | |
|---|---|
| .onAttach | Source code |
| QPforSig | Man page Source code |
| addBestSignatureToSubset | Man page Source code |
| adjustAlexandrovSignature | Man page Source code |
| adjustShiraishiSignature | Man page Source code |
| adjustSignaturesForRegionSet | Man page Source code |
| buildGenomesFromMutationData | Man page Source code |
| buildSortedAlexandrovSignaturePatternList | Man page Source code |
| compNucFreq | Man page Source code |
| composeGenomesFromExposures | Man page Source code |
| computeExplainedVariance | Man page Source code |
| computeFrobeniusNorm | Man page Source code |
| computeRSS | Man page Source code |
| convAlx2Shi | Man page Source code |
| convertAlexandrov2Shiraishi | Man page Source code |
| convertGenomesFromVRanges | Man page Source code |
| convertSeqFreqToBaseFreq | Man page Source code |
| decompTumor2Sig | Man page |
| decompTumor2Sig-package | Man page |
| decomposeTumorGenomes | Man page Source code |
| determineSignatureDistances | Man page Source code |
| determineTypeNumBasesAndTrDir | Man page Source code |
| downgradeShiraishiSignatures | Man page Source code |
| evaluateDecompositionQuality | Man page Source code |
| getBestDecomp4Ksignatures | Man page Source code |
| getCountData | Man page Source code |
| getFeatVectList | Man page Source code |
| getGenomesFromMutFeatData | Man page Source code |
| getNumFlankingBases | Man page Source code |
| getNumSignatures | Man page Source code |
| getSampleList | Man page Source code |
| getSigFeatDist | Man page Source code |
| getSigFromEstParam | Man page Source code |
| getSigType | Man page Source code |
| getSignaturesFromEstParam | Man page Source code |
| haveTrDir | Man page Source code |
| is.probability.data.frame | Man page Source code |
| is.probability.data.frame.list | Man page Source code |
| is.probability.matrix | Man page Source code |
| is.probability.matrix.list | Man page Source code |
| is.probability.object | Man page Source code |
| is.probability.vector | Man page Source code |
| is.probability.vector.list | Man page Source code |
| isAlexandrovSet | Man page Source code |
| isBackGround | Man page Source code |
| isEstParamObject | Man page Source code |
| isExposureSet | Man page Source code |
| isMutFeatDataObject | Man page Source code |
| isShiraishiSet | Man page Source code |
| isSignatureSet | Man page Source code |
| mapSignatureSets | Man page Source code |
| plotAlexandrovModel | Man page Source code |
| plotDecomposedContribution | Man page Source code |
| plotExplainedVariance | Man page Source code |
| plotMutationDistribution | Man page Source code |
| plotShiraishiModel | Man page Source code |
| processMultipleSigSets | Man page Source code |
| readAlexandrovSignatures | Man page Source code |
| readGenomesFromMPF | Man page Source code |
| readGenomesFromVCF | Man page Source code |
| readShiraishiSignatures | Man page Source code |
| roundIntegerSum | Man page Source code |
| sameSignatureFormat | Man page Source code |
| setNames4ShiraishiTable | Man page Source code |
| setNumFlankingBases | Man page Source code |
| setSigFeatDist | Man page Source code |
| setSigType | Man page Source code |
| setTrDir | Man page Source code |
