isExposureSet: isExposureSet

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

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: <[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
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)

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