oligo (version 1.36.1)

getSequenceLengths: Load chromosome sequence lengths for UCSC genome build hg18 or hg19

Description

Load chromosome sequence lengths for UCSC genome build hg18 or hg19

Usage

getSequenceLengths(build)

Arguments

build

character string: "hg18" or "hg19"

Value

• Names integer vector of chromosome lengths.

Details

The chromosome sequence lengths for UCSC builds hg18 and hg19 were extracted from the packages BSgenome.Hsapiens.UCSC.hg18 and BSgenome.Hsapiens.UCSC.hg19, respectively.

Examples

getSequenceLengths("hg18")
getSequenceLengths("hg19")

if(require("GenomicRanges")){
## from GenomicRanges
	sl <- getSequenceLengths("hg18")[c("chr1", "chr2", "chr3")]
	gr <-
		GRanges(seqnames =
			Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
			ranges =
			IRanges(1:10, width = 10:1, names = head(letters,10)),
			strand =
			Rle(strand(c("-", "+", "*", "+", "-")),
			    c(1, 2, 2, 3, 2)),
			score = 1:10,
			GC = seq(1, 0, length=10),
			seqlengths=sl)
	metadata(gr) <- list(genome="hg18")
	gr
	metadata(gr)
}