# Decomposition of individual tumors into mutational signatures by signature refitting

## Documentation for package ‘decompTumor2Sig’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

decompTumor2Sig-package | decompTumor2Sig - Decomposition of individual tumors into mutational signatures by signature refitting
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
decomposeTumorGenomes | Decompose tumor genomes into mutational signatures
decompTumor2Sig | decompTumor2Sig - Decomposition of individual tumors into mutational signatures by signature refitting
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