getSequenceLengths {oligoClasses} | R Documentation |
Load chromosome sequence lengths for UCSC genome build hg18 or hg19
getSequenceLengths(build)
build |
character string: "hg18" or "hg19" |
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.
Names integer vector of chromosome lengths.
R. Scharpf
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) }