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

Description Details Author(s) References


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.


Package: decompTumor2Sig
Type: Package
Version: 2.5.1
Date: 2020-07-27
License: GPL (>=2)

The package provides the following functions:

composeGenomesFromExposures(): (re-)construct tumor genome mutation
frequencies from the signatures and
their corresponding exposures, or
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
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,
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
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
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.


Rosario M. Piro, Politecnico di Milano [aut, cre]
Sandra Krueger, Freie Universitaet Berlin [ctb]
Maintainer: Rosario M. Piro
E-Mail: <> or <>

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

decompTumor2Sig documentation built on Nov. 8, 2020, 8:23 p.m.