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

Run this code

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)
}

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