decompTumor2Sig-package: decompTumor2Sig - Decomposition of individual tumors into...

In rmpiro/decompTumor2Sig: Decomposition of individual tumors into mutational signatures by signature refitting

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:	2.13.1
Date:	2022-05-09
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: <[e-mail]> or <[e-mail]>

References

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

rmpiro/decompTumor2Sig documentation built on May 15, 2022, 3:27 a.m.