cleanSeqlevels: Cleans and standardizes chromosomal information.

In J0bbie/R2CPCT: Misc. functions to perform import and analysis of WGS and RNA-Seq samples

Description

Removes unused chromosomes, converts seqlevels to UCSC nomenclature and adds chromosomal information.

Usage

cleanSeqlevels(g, excludeChr = NULL)

Arguments

g	(GRanges): GRanges object to be cleaned.
excludeChr	(character): Character vector of chromosomes which should be excluded, e.g. 'chrY' if patient is female or chrM. Set NULL to ignore.

Value

(GRanges) Returns cleaned-up GRanges.

Author(s)

Job van Riet [e-mail]

Examples

 gr0 <- GenomicRanges::GRanges(
 S4Vectors::Rle(c('chr2', 'chr2', 'chr1', 'chr3'), c(1, 3, 2, 4)), 
 IRanges::IRanges(1:10, width=10:1)
 )
	gr0.clean <- cleanSeqlevels(gr0)

	GenomeInfoDb::seqinfo(gr0.clean)

J0bbie/R2CPCT documentation built on Feb. 24, 2022, 8:15 a.m.