convertAlexandrov2Shiraishi: Convert Alexandrov-type signatures to Shiraishi signatures

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

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
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
readAlexandrovSignatures
readShiraishiSignatures

Examples

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

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

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