Files in rmpiro/decompTumor2Sig

Decomposition of individual tumors into mutational signatures by signature refitting

R/QPforSig.R R/addBestSignatureToSubset.R R/adjustSignaturesForRegionSet.R R/buildGenomesFromMutationData.R R/buildSortedAlexandrovSignaturePatternList.R R/composeGenomesFromExposures.R R/computeExplainedVariance.R R/convAlx2Shi.R R/convertAlexandrov2Shiraishi.R R/convertGenomesFromVRanges.R R/decompTumor2Sig-package.R R/decomposeTumorGenomes.R R/determineSignatureDistances.R R/determineTypeNumBasesAndTrDir.R R/downgradeShiraishiSignatures.R R/evaluateDecompositionQuality.R R/external_classes_wrapper_functions.R R/getBestDecomp4Ksignatures.R R/getGenomesFromMutFeatData.R R/getSignaturesFromEstParam.R R/helper_functions_for_class_checks.R R/helper_functions_for_sequences.R R/mapSignatureSets.R R/mathematical_functions.R R/onAttach.R R/plotAlexandrovModel.R R/plotDecomposedContribution.R R/plotExplainedVariance.R R/plotMutationDistribution.R R/plotShiraishiModel.R R/processMultipleSigSets.R R/readAlexandrovSignatures.R R/readGenomesFromMPF.R R/readGenomesFromVCF.R R/readShiraishiSignatures.R R/setNames4ShiraishiTable.R README.md decompTumor2Sig-manual.pdf inst/script/Alexandrov_PMID_23945592_435_tumors-pmsignature-15sig.R inst/script/Nik-Zainal_PMID_22608084-genomes.R inst/script/Nik-Zainal_PMID_22608084-pmsignature.R man/QPforSig.Rd man/addBestSignatureToSubset.Rd man/adjustAlexandrovSignature.Rd man/adjustShiraishiSignature.Rd man/adjustSignaturesForRegionSet.Rd man/buildGenomesFromMutationData.Rd man/buildSortedAlexandrovSignaturePatternList.Rd man/compNucFreq.Rd man/composeGenomesFromExposures.Rd man/computeExplainedVariance.Rd man/computeFrobeniusNorm.Rd man/computeRSS.Rd man/convAlx2Shi.Rd man/convertAlexandrov2Shiraishi.Rd man/convertGenomesFromVRanges.Rd man/convertSeqFreqToBaseFreq.Rd man/decompTumor2Sig-package.Rd man/decomposeTumorGenomes.Rd man/determineSignatureDistances.Rd man/determineTypeNumBasesAndTrDir.Rd man/downgradeShiraishiSignatures.Rd man/evaluateDecompositionQuality.Rd man/getBestDecomp4Ksignatures.Rd man/getCountData.Rd man/getFeatVectList.Rd man/getGenomesFromMutFeatData.Rd man/getNumFlankingBases.Rd man/getNumSignatures.Rd man/getSampleList.Rd man/getSigFeatDist.Rd man/getSigFromEstParam.Rd man/getSigType.Rd man/getSignaturesFromEstParam.Rd man/haveTrDir.Rd man/is.probability.data.frame.Rd man/is.probability.data.frame.list.Rd man/is.probability.matrix.Rd man/is.probability.matrix.list.Rd man/is.probability.object.Rd man/is.probability.vector.Rd man/is.probability.vector.list.Rd man/isAlexandrovSet.Rd man/isBackGround.Rd man/isEstParamObject.Rd man/isExposureSet.Rd man/isMutFeatDataObject.Rd man/isShiraishiSet.Rd man/isSignatureSet.Rd man/mapSignatureSets.Rd man/plotAlexandrovModel.Rd man/plotDecomposedContribution.Rd man/plotExplainedVariance.Rd man/plotMutationDistribution.Rd man/plotShiraishiModel.Rd man/processMultipleSigSets.Rd man/readAlexandrovSignatures.Rd man/readGenomesFromMPF.Rd man/readGenomesFromVCF.Rd man/readShiraishiSignatures.Rd man/roundIntegerSum.Rd man/sameSignatureFormat.Rd man/setNames4ShiraishiTable.Rd man/setNumFlankingBases.Rd man/setSigFeatDist.Rd man/setSigType.Rd man/setTrDir.Rd vignettes/decompTumor2Sig.Rmd