getSignaturesFromEstParam {decompTumor2Sig} | R Documentation

## Get signatures from an `EstimatedParameters` object.

### 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 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`
`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)

[Package decompTumor2Sig version 2.0.0 Index]