getGenomesFromMutFeatData {decompTumor2Sig} | R Documentation

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

### 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`

### 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)

[Package decompTumor2Sig version 2.0.0 Index]