getSignaturesFromEstParam: Get signatures from an 'EstimatedParameters' object.

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

Description

'getSignaturesFromEstParam()' takes an EstimatedParameters object (signatures data) as computed by the 'pmsignature' package (by pmsignature::getPMSignature; version 0.3.0) and extracts the signature information. The signatures can then be passed to decomposeTumorGenomes.

Usage

getSignaturesFromEstParam(Param)

Arguments

Param

(Mandatory) A pmsignature::EstimatedParameters object as those produced by the de novo signature construction method pmsignature::getPMSignature.

Value

A list of Shiraishi signatures, one object per signature. Please see readShiraishiSignatures or the decompTumor2Sig vignette for more information on the format of Shiraishi signatures.

Author(s)

Rosario M. Piro, Politecnico di Milano
Sandra Krueger, Freie Universitaet Berlin
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
readShiraishiSignatures

Examples

### load signatures for breast cancer genomes from 
### Nik-Zainal et al (PMID: 22608084) in the format produced by
### pmsignature (PMID: 26630308)
pmsigdata <- system.file("extdata",
         "Nik-Zainal_PMID_22608084-pmsignature-Param.Rdata", 
         package="decompTumor2Sig")
load(pmsigdata)

### extract the signatures from the pmsignature Param object
signatures <- getSignaturesFromEstParam(Param)

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