gr.chr: Prepend "chr" to 'GRanges seqlevels'

In mskilab/gUtils: R Package Providing Additional Capabilities and Speed for GenomicRanges Operations

Prepend "chr" to GRanges seqlevels

Description

Prepend "chr" to GRanges seqlevels

Usage

gr.chr(gr)

Arguments

gr	GRanges object to append 'chr' to

Details

implementation looks for strings that begin with 0-9, X,Y,M, or Un for the unmapped chromosome regions/decoys. regex pattern: "^([0-9,X, Y, M,x,y,m, Un, EBV]+)" replacement pattern: "chr\1"

Value

Identical GRanges, but with 'chr' prepended to each seqlevel

Author(s)

Max Chao

Examples

gr <- gr.chr(GRanges(c(1,"chrX"), IRanges(c(1,2), 1)))
seqnames(gr)

mskilab/gUtils documentation built on March 5, 2025, 11:51 p.m.