composeGenomesFromExposures: Compose tumor genomes from exposures.

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

Description

'composeGenomesFromExposures()' re-composes (or predicts) tumor genomes (i.e., their mutation frequencies) from the given mutational signatures and their corresponding exposures, or contributions. The (re-)composition is performed by computing the weighted sum of the mutational signatures, where the weights are the exposures (=contributions) of the corresponding signatures. This can, for example, be used to verify that a decomposition obtained from decomposeTumorGenomes is meaningful.

Usage

composeGenomesFromExposures(exposures, signatures)

Arguments

exposures	(Mandatory) A single vector or list of vectors containing the estimated signature contributions/exposures as computed by the function decomposeTumorGenomes. A list of vectors is used if the (re-)composition shall be performed for multiple genomes. The number of elements of each exposure vector must correspond to the number of signatures.
signatures	(Mandatory) The list of signatures (vectors, data frames or matrices) for which the exposures were obtained. Each of the list objects represents one mutational signature. Vectors are used for Alexandrov signatures, data frames or matrices for Shiraishi signatures.

Value

A list of "predicted" genomes, i.e., the frequencies of their mutational patterns computed as weighted sums of the mutational signatures, where the weights correspond to the contributions of, i.e., exposures to, the corresponding signatures.

Author(s)

Rosario M. Piro
Politecnico di Milano
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.

See Also

decompTumor2Sig
decomposeTumorGenomes

Examples

### get Alexandrov signatures from COSMIC
signatures <- readAlexandrovSignatures()

### load preprocessed breast cancer genomes (object 'genomes') from
### Nik-Zainal et al (PMID: 22608084) 
gfile <- system.file("extdata",
         "Nik-Zainal_PMID_22608084-genomes-Alexandrov_3bases.Rdata", 
         package="decompTumor2Sig")
load(gfile)

### compute exposures
exposures <- decomposeTumorGenomes(genomes, signatures, verbose=FALSE)

### re-compose (predict) tumor genome features from exposures
predGenomes <- composeGenomesFromExposures(exposures, signatures)

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