getGenomesFromMutFeatData: Get genomes (mutation frequencies) from...

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

Get genomes (mutation frequencies) from MutationFeatureData.

Description

'getGenomesFromMutFeatData()' takes a MutationFeatureData object (mutation count data) as read by the 'pmsignature' package (e.g., by pmsignature::readMPFile, version 0.3.0) and extracts the mutation counts of the genomes therein. For passing the genomes to decomposeTumorGenomes, the mutation counts must be normalized to mutation frequencies, which is done by default. [IMPORTANT: set normalize to FALSE only if you are interested in full integer counts, but do not pass unnormalized counts to decomposeTumorGenomes!]

Usage

getGenomesFromMutFeatData(mutFeatData, normalize=TRUE)

Arguments

mutFeatData	(Mandatory) A MutationFeatureData object as constructed, for example, by pmsignature::readMPFile.
normalize	(Optional) Boolean value to specify whether to normalize the mutation count data to mutation fractions between 0 and 1. This is the default and NECESSARY in case you want to pass the return value to decomposeTumorGenomes. Set normalize to FALSE only if you are interested in full integer counts, but do not pass unnormalized counts to decomposeTumorGenomes!

Value

A list of mutation frequencies (or mutation counts if not normalized), one object per genome. The format is either according to the Shiraishi or the Alexandrov model, depending on how the mutation data was loaded with pmsignature.

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

Examples

### get 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-G.Rdata", 
         package="decompTumor2Sig")
load(pmsigdata)

### extract the genomes from the pmsignature G object
genomes <- getGenomesFromMutFeatData(G, normalize=TRUE)

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