isExposureSet {decompTumor2Sig} | R Documentation

## isExposureSet

### Description

'isExposureSet()' checks whether the input object is a set (list) of numeric objects compatible with exposure output obtained from `decomposeTumorGenomes`.

### Usage

    isExposureSet(x)

### Arguments

`x` | Object to be checked.

### Value

Logical value (true or false).

### Author(s)

Rosario M. Piro
Politecnico di Milano
Maintainer: Rosario M. Piro
E-Mail: <rmpiro@gmail.com> or <rosariomichael.piro@polimi.it>

### 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`
`decomposeTumorGenomes`

### Examples

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

    ### load reference genome
    refGenome <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19

    ### read breast cancer genomes from Nik-Zainal et al (PMID: 22608084)
    gfile <- system.file("extdata",
             "Nik-Zainal_PMID_22608084-VCF-convertedfromMPF.vcf.gz",
             package="decompTumor2Sig")
    genomes <- readGenomesFromVCF(gfile, numBases=3, type="Alexandrov",
             trDir=FALSE, refGenome=refGenome, verbose=FALSE)

    ### compute exposures
    exposures <- decomposeTumorGenomes(genomes, signatures, verbose=FALSE)

    isExposureSet(exposures)

[Package decompTumor2Sig version 2.6.0 Index]