Man pages for rmpiro/decompTumor2Sig
Decomposition of individual tumors into mutational signatures by signature refitting
| addBestSignatureToSubset | addBestSignatureToSubset (internal function) |
| adjustAlexandrovSignature | Adjust an Alexandrov signature (internal function) |
| adjustShiraishiSignature | Adjust an Shiraishi signature (internal function) |
| adjustSignaturesForRegionSet | Adjust (normalize) signatures for a set of genomic regions. |
| buildGenomesFromMutationData | buildGenomesFromMutationData (internal function) |
| buildSortedAlexandrovSignaturePatternList | buildSortedAlexandrovSignaturePatternList (internal function) |
| compNucFreq | Compute nucleotide frequencies (internal function) |
| composeGenomesFromExposures | Compose tumor genomes from exposures. |
| computeExplainedVariance | Compute the explained variance. |
| computeFrobeniusNorm | computeFrobeniusNorm (internal function) |
| computeRSS | computeRSS (internal function) |
| convAlx2Shi | convAlx2Shi (internal function) |
| convertAlexandrov2Shiraishi | Convert Alexandrov-type signatures to Shiraishi signatures |
| convertGenomesFromVRanges | Convert genomes from a 'VRanges' object |
| convertSeqFreqToBaseFreq | Convert sequence pattern frequencies to base frequencies... |
| decomposeTumorGenomes | Decompose tumor genomes into mutational signatures |
| decompTumor2Sig-package | decompTumor2Sig - Decomposition of individual tumors into... |
| determineSignatureDistances | Determine differences between a given signature and a set of... |
| determineTypeNumBasesAndTrDir | determineTypeNumBasesAndTrDir (internal function) |
| downgradeShiraishiSignatures | Downgrade Shiraishi-type signatures. |
| evaluateDecompositionQuality | Evaluate tumor decomposition quality. |
| getBestDecomp4Ksignatures | getBestDecomp4Ksignatures (internal function) |
| getCountData | getCountData (internal function) |
| getFeatVectList | getFeatVectList (internal function) |
| getGenomesFromMutFeatData | Get genomes (mutation frequencies) from... |
| getNumFlankingBases | getNumFlankingBases (internal function) |
| getNumSignatures | getNumSignatures (internal function) |
| getSampleList | getSampleList (internal function) |
| getSigFeatDist | getSigFeatDist (internal function) |
| getSigFromEstParam | getSigFromEstParam (internal function) |
| getSignaturesFromEstParam | Get signatures from an 'EstimatedParameters' object. |
| getSigType | getSigType (internal function) |
| haveTrDir | haveTrDir (internal function) |
| isAlexandrovSet | isAlexandrovSet |
| isBackGround | isBackGround (internal function) |
| isEstParamObject | isEstParamObject (internal function) |
| isExposureSet | isExposureSet |
| isMutFeatDataObject | isMutFeatDataObject (internal function) |
| is.probability.data.frame | is.probability.data.frame (internal function) |
| is.probability.data.frame.list | is.probability.data.frame.list (internal function) |
| is.probability.matrix | is.probability.matrix (internal function) |
| is.probability.matrix.list | is.probability.matrix.list (internal function) |
| is.probability.object | is.probability.object (internal function) |
| is.probability.vector | is.probability.vector (internal function) |
| is.probability.vector.list | is.probability.vector.list (internal function) |
| isShiraishiSet | isShiraishiSet |
| isSignatureSet | isSignatureSet |
| mapSignatureSets | Map one signature set to another. |
| plotAlexandrovModel | plotAlexandrovModel (internal function) |
| plotDecomposedContribution | Plot the decomposition (contributions/exposures) of a tumor... |
| plotExplainedVariance | Plot the explained variance as a function of the number of... |
| plotMutationDistribution | Plot mutation frequency data of a mutational signature or... |
| plotShiraishiModel | plotShiraishiModel (internal function) |
| processMultipleSigSets | processMultipleSigSets (internal function) |
| QPforSig | QPforSig (internal function) |
| readAlexandrovSignatures | Read Alexandrov-type signatures (COSMIC format). |
| readGenomesFromMPF | Read tumor genomes from an MPF file (Mutation Position... |
| readGenomesFromVCF | Read tumor genomes from a VCF file (Variant Call Format). |
| readShiraishiSignatures | Read a set of Shiraishi signatures. |
| roundIntegerSum | roundIntegerSum (internal function) |
| sameSignatureFormat | sameSignatureFormat |
| setNames4ShiraishiTable | setNames4ShiraishiTable (internal function) |
| setNumFlankingBases | setNumFlankingBases (internal function) |
| setSigFeatDist | setSigFeatDist (internal function) |
| setSigType | setSigType (internal function) |
| setTrDir | setTrDir (internal function) |
