Man pages for decompTumor2Sig
Decomposition of individual tumors into mutational signatures by signature refitting

addBestSignatureToSubsetaddBestSignatureToSubset (internal function)
buildGenomesFromMutationDatabuildGenomesFromMutationData (internal function)
buildSortedAlexandrovSignaturePatternListbuildSortedAlexandrovSignaturePatternList (internal function)
composeGenomesFromExposuresCompose tumor genomes from exposures.
computeExplainedVarianceCompute the explained variance.
computeFrobeniusNormcomputeFrobeniusNorm (internal function)
computeRSScomputeRSS (internal function)
convAlx2ShiconvAlx2Shi (internal function)
convertAlexandrov2ShiraishiConvert Alexandrov-type signatures to Shiraishi signatures
convertGenomesFromVRangesConvert genomes from a 'VRanges' object
decomposeTumorGenomesDecompose tumor genomes into mutational signatures
decompTumor2Sig-packagedecompTumor2Sig - Decomposition of individual tumors into...
determineSignatureDistancesDetermine differences between a given signature and a set of...
determineTypeNumBasesAndTrDirdetermineTypeNumBasesAndTrDir (internal function)
downgradeShiraishiSignaturesDowngrade Shiraishi-type signatures.
evaluateDecompositionQualityEvaluate tumor decomposition quality.
getBestDecomp4KsignaturesgetBestDecomp4Ksignatures (internal function)
getCountDatagetCountData (internal function)
getFeatVectListgetFeatVectList (internal function)
getGenomesFromMutFeatDataGet genomes (mutation frequencies) from...
getNumFlankingBasesgetNumFlankingBases (internal function)
getNumSignaturesgetNumSignatures (internal function)
getSampleListgetSampleList (internal function)
getSigFeatDistgetSigFeatDist (internal function)
getSigFromEstParamgetSigFromEstParam (internal function)
getSignaturesFromEstParamGet signatures from an 'EstimatedParameters' object.
getSigTypegetSigType (internal function)
haveTrDirhaveTrDir (internal function)
isAlexandrovSetisAlexandrovSet
isBackGroundisBackGround (internal function)
isEstParamObjectisEstParamObject (internal function)
isExposureSetisExposureSet
isMutFeatDataObjectisMutFeatDataObject (internal function)
is.probability.data.frameis.probability.data.frame (internal function)
is.probability.data.frame.listis.probability.data.frame.list (internal function)
is.probability.matrixis.probability.matrix (internal function)
is.probability.matrix.listis.probability.matrix.list (internal function)
is.probability.objectis.probability.object (internal function)
is.probability.vectoris.probability.vector (internal function)
is.probability.vector.listis.probability.vector.list (internal function)
isShiraishiSetisShiraishiSet
isSignatureSetisSignatureSet
mapSignatureSetsMap one signature set to another.
plotAlexandrovModelplotAlexandrovModel (internal function)
plotDecomposedContributionPlot the decomposition (contributions/exposures) of a tumor...
plotExplainedVariancePlot the explained variance as a function of the number of...
plotMutationDistributionPlot mutation frequency data of a mutational signature or...
plotShiraishiModelplotShiraishiModel (internal function)
processMultipleSigSetsprocessMultipleSigSets (internal function)
QPforSigQPforSig (internal function)
readAlexandrovSignaturesRead Alexandrov-type signatures (COSMIC format).
readGenomesFromMPFRead tumor genomes from an MPF file (Mutation Position...
readGenomesFromVCFRead tumor genomes from a VCF file (Variant Call Format).
readShiraishiSignaturesRead a set of Shiraishi signatures.
roundIntegerSumroundIntegerSum (internal function)
sameSignatureFormatsameSignatureFormat
setNames4ShiraishiTablesetNames4ShiraishiTable (internal function)
setNumFlankingBasessetNumFlankingBases (internal function)
setSigFeatDistsetSigFeatDist (internal function)
setSigTypesetSigType (internal function)
setTrDirsetTrDir (internal function)
decompTumor2Sig documentation built on Nov. 8, 2020, 8:23 p.m.