decompTumor2Sig-package {decompTumor2Sig} | R Documentation

## decompTumor2Sig - Decomposition of individual tumors into mutational signatures by signature refitting

### Description

The decompTumor2Sig package uses quadratic programming to decompose the somatic mutation catalog from an individual tumor sample (or multiple individual tumor samples) into a set of given mutational signatures (either of the "Alexandrov model" by Alexandrov et al, Nature 500(7463):415-421, 2013, or the "Shiraishi model" by Shiraishi et al, PLoS Genet 11(12):e1005657, 2015), thus computing weights (or "exposures") that reflect the contributions of the signatures to the mutation load of the tumor.

### Details

Package: | decompTumor2Sig
Type: | Package
Version: | 2.7.3
Date: | 2021-04-01
License: | GPL (>=2)

The package provides the following functions:

adjustSignaturesForRegionSet(): | adjust (normalize) mutational
| signatures for use with mutation data from a
| specific, limited subset of genomic regions
| (e.g., for targetted sequencing).
composeGenomesFromExposures(): | (re-)construct tumor genome mutation
| frequencies from the signatures and
| their corresponding exposures, or
| contributions.
computeExplainedVariance(): | determine the variance explained by
| estimated signature contributions
| (i.e., exposures to signatures).
convertAlexandrov2Shiraishi(): | convert a set of Alexandrov
| signatures to Shiraishi signatures.
convertGenomesFromVRanges(): | convert a genome or set of genomes
| from a `VariantAnnotation::VRanges`
| object.
decomposeTumorGenomes(): | determine the weights/contributions of
| a set of signatures to each of a set of
| individual tumor genomes.
determineSignatureDistances(): | for a given signature
| compute its distances to each of a set
| of target signatures.
downgradeShiraishiSignatures(): | downgrade Shiraishi signatures
| by removing flanking bases and/or the
| transcription direction.
evaluateDecompositionQuality(): | evaluate the quality of a
| decomposition by comparing the
| re-composed (=re-constructed) tumor
| mutation frequencies to those actually
| observed in the tumor genome.
getGenomesFromMutFeatData(): | extract the genomes from a
| `MutationFeatureData` object as
| provided by, for example,
| `pmsignature::readMPFile`.
getSignaturesFromEstParam(): | extract a set of signatures from an
| `EstimatedParameters` object as
| returned by function `getPMSignature`
| of the `pmsignature` package.
isAlexandrovSet(): | checks whether the input list is
| compatible with the Alexandrov format
| (probability vectors).
isExposureSet(): | checks whether the input list is
| compatible with exposure output obtained
| from `decomposeTumorGenomes`.
isShiraishiSet(): | checks whether the input list is
| compatible with the Shiraishi format
| (matrices or data.frames of
| probabilities).
isSignatureSet(): | checks whether the input list is
| compatible with either the Alexandrov
| or Shiraishi format.
mapSignatureSets(): | find a mapping from one signature
| set to another.
plotDecomposedContribution(): | plot the decomposition of a
| genome into mutational signatures
| (i.e., the contributions of, or
| exposures to, the signatures).
plotExplainedVariance(): | plot the variance of a genome's
| mutation patterns which can be
| explained with an increasing number
| of signatures.
plotMutationDistribution(): | plot a single signature or the
| mutation frequency data for a single
| genome.
readAlexandrovSignatures(): | read Alexandrov signatures in the
| COSMIC format from a flat file or URL.
readGenomesFromMPF(): | read a genome or set of genomes from a
| Mutation Position Format (MPF) file.
readGenomesFromVCF(): | read a genome or set of genomes from a
| Variant Call Format (VCF) file.
readShiraishiSignatures(): | read Shiraishi signatures from
| flat files.
sameSignatureFormat(): | checks whether two input lists are sets
| of signatures of the same format.

### Author(s)

Rosario M. Piro, Politecnico di Milano [aut, cre]
Sandra Krueger, Freie Universitaet Berlin [ctb]
Maintainer: Rosario M. Piro
E-Mail: <rmpiro@gmail.com> or <rosariomichael.piro@polimi.it>

### References

http://rmpiro.net/decompTumor2Sig/
Krueger, Piro (2019) decompTumor2Sig: Identification of mutational signatures active in individual tumors. BMC Bioinformatics 20(Suppl 4):152.

[Package decompTumor2Sig version 2.10.0 Index]