downgradeShiraishiSignatures: Downgrade Shiraishi-type signatures.

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

Downgrade Shiraishi-type signatures.

Description

'downgradeShiraishiSignatures()' downgrades/trims signatures of the Shiraishi type by discarding flanking bases (reducing the length of the sequence pattern) and/or the transcription direction. The downgrade doesn't pose a problem because the flanking bases and the transcription direction are considered as independent features according to the Shiraishi model of mutational signatures.

Usage

downgradeShiraishiSignatures(signatures, numBases=NULL,
removeTrDir=FALSE)

Arguments

signatures	(Mandatory) A list of Shiraishi signatures that need to be downgraded/trimmed.
numBases	(Conditionally optional) The total number of bases (mutated base plus flanking bases around the mutated base) that should be kept. All further flanking bases farther away from the mutated bases are dropped. If specified, numBases must be odd and smaller than the current number of bases of the signatures. If NULL, no flanking bases will be dropped. At least one of numBases or removeTrDir must be specified.
removeTrDir	(Conditionally optional) Logical value that specifies whether information on the transcript direction should be dropped (if present at all). At least one of numBases or removeTrDir must be specified.

Value

A list of Shiraishi signatures that have been accordingly downgraded.

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

Examples

### Load 15 Shiraishi signatures obtained from 435 tumor genomes from
### Alexandrov et al. (number of bases: 5, transcription direction: yes)
sfile <- system.file("extdata",
         "Alexandrov_PMID_23945592_435_tumors-pmsignature-15sig.Rdata", 
         package="decompTumor2Sig")
load(sfile)

### downgrade the signatures to include only 3 bases and drop the
### transcription direction 
downgradeShiraishiSignatures(signatures, numBases=3, removeTrDir=TRUE)

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