downgradeShiraishiSignatures {decompTumor2Sig} | R Documentation

## 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
Freie Universitaet Berlin
Maintainer: Rosario M. Piro
E-Mail: <rmpiro@gmail.com> or <r.piro@fu-berlin.de>

### References

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.

### 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)

[Package decompTumor2Sig version 2.0.0 Index]