sameSignatureFormat: sameSignatureFormat

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

sameSignatureFormat

Description

'sameSignatureFormat()' checks whether two input object are sets (lists) of numeric objects both compatible with the same signature format (probability vectors for Alexandrov signatures and probability matrices or data.frames for Shiraishi signatures). For Shiraishi signatures also the number of flanking bases and the presence of transcription-strand information are compared. For Alexandrov signatures also the number of triplet changes are compared.

Usage

sameSignatureFormat(x, y)

Arguments

x	First object to be checked.
y	Second object to be checked.

Value

Logical value (true or false).

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
isAlexandrovSet
isShiraishiSet

Examples

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

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

sameSignatureFormat(signAlexandrov, signShiraishi)

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