Decomposition of individual tumors into mutational signatures by signature refitting

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Documentation for package ‘decompTumor2Sig’ version 2.22.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
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decompTumor2Sig-package	decompTumor2Sig - Decomposition of individual tumors into mutational signatures by signature refitting
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
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