adjustSignaturesForRegionSet
                        Adjust (normalize) signatures for a set of
                        genomic regions.
composeGenomesFromExposures
                        Compose tumor genomes from exposures.
computeExplainedVariance
                        Compute the explained variance.
convertAlexandrov2Shiraishi
                        Convert Alexandrov-type signatures to Shiraishi
                        signatures
convertGenomesFromVRanges
                        Convert genomes from a 'VRanges' object
decompTumor2Sig-package
                        decompTumor2Sig - Decomposition of individual
                        tumors into mutational signatures by signature
                        refitting
decomposeTumorGenomes   Decompose tumor genomes into mutational
                        signatures
determineSignatureDistances
                        Determine differences between a given signature
                        and a set of target signatures.
downgradeShiraishiSignatures
                        Downgrade Shiraishi-type signatures.
evaluateDecompositionQuality
                        Evaluate tumor decomposition quality.
getGenomesFromMutFeatData
                        Get genomes (mutation frequencies) from
                        'MutationFeatureData'.
getSignaturesFromEstParam
                        Get signatures from an 'EstimatedParameters'
                        object.
isAlexandrovSet         isAlexandrovSet
isExposureSet           isExposureSet
isShiraishiSet          isShiraishiSet
isSignatureSet          isSignatureSet
mapSignatureSets        Map one signature set to another.
plotDecomposedContribution
                        Plot the decomposition
                        (contributions/exposures) of a tumor genome.
plotExplainedVariance   Plot the explained variance as a function of
                        the number of signatures
plotMutationDistribution
                        Plot mutation frequency data of a mutational
                        signature or tumor genome.
readAlexandrovSignatures
                        Read Alexandrov-type signatures (COSMIC
                        format).
readGenomesFromMPF      Read tumor genomes from an MPF file (Mutation
                        Position Format).
readGenomesFromVCF      Read tumor genomes from a VCF file (Variant
                        Call Format).
readShiraishiSignatures
                        Read a set of Shiraishi signatures.
sameSignatureFormat     sameSignatureFormat
