downgradeShiraishiSignatures {decompTumor2Sig} | R Documentation |
'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.
downgradeShiraishiSignatures(signatures, numBases=NULL, removeTrDir=FALSE)
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, |
removeTrDir |
(Conditionally optional) Logical value that specifies
whether information on the transcript direction should be dropped (if
present at all). At least one of |
A list of Shiraishi signatures that have been accordingly downgraded.
Rosario M. Piro
Freie Universitaet Berlin
Maintainer: Rosario
M. Piro
E-Mail: <rmpiro@gmail.com> or <r.piro@fu-berlin.de>
http://rmpiro.net/decompTumor2Sig/
Krueger, Piro (2018) decompTumor2Sig: Identification of mutational
signatures active in individual tumors. BMC Bioinformatics (accepted for
publication).
Krueger, Piro (2017) Identification of Mutational Signatures Active in
Individual Tumors. NETTAB 2017 - Methods, Tools & Platforms for
Personalized Medicine in the Big Data Era, October 16-18, 2017, Palermo,
Italy. PeerJ Preprints 5:e3257v1, 2017.
### 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)