convertAlexandrov2Shiraishi {decompTumor2Sig} | R Documentation

## Convert Alexandrov-type signatures to Shiraishi signatures

### Description

'convertAlexandrov2Shiraishi()' converts a set Alexandrov signatures to the Shiraishi model, summing the respective frequencies of base changes, and upstream and downstream flanking bases. In most cases, the resulting Shiraishi signatures don't provide information on the transcription strand, as this is not part of the standard Alexandrov signatures. While the conversion is mainly thought for signatures, it actually works also for mutation frequency data from genomes which have the same format. [Attention: this conversion entails a loss of specificity and the applicability of Shiraishi signatures derived from Alexandrov signatures has not been extensively explored!]

### Usage

    convertAlexandrov2Shiraishi(signatures)

### Arguments

`signatures` | (Mandatory) A list of Alexandrov signatures with named elements as produced by `readAlexandrovSignatures`.

### Value

A list of Shiraishi signatures that can be used for `decomposeTumorGenomes`.

### Author(s)

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

### 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`
`readAlexandrovSignatures`
`readShiraishiSignatures`

### Examples

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

    ### convert them to the Shiraishi model
    signShiraishi <- convertAlexandrov2Shiraishi(signAlexandrov)

[Package decompTumor2Sig version 2.0.0 Index]