Hello, Is there a neater way to import an entire chromosome ? uniqueness <- import("mapabilityAlign36mer.bigWig", which = GRanges("chr5", IRanges(1, end = .Machine$integer.max - 1))) GenomicSelection requires a correctly specified genome argument, which I'm unsure of how to obtain from the bigWig file in R. -------------------------------------- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia

On 03/05/2014 05:00 PM, Dario Strbenac wrote: > Hello, > > Is there a neater way to import an entire chromosome ? > > uniqueness <- import("mapabilityAlign36mer.bigWig", which = GRanges("chr5", IRanges(1, end = .Machine$integer.max - 1))) > > GenomicSelection requires a correctly specified genome argument, which I'm unsure of how to obtain from the bigWig file in R. > A BigWigFile knows about seqinfo(), so test_bw <- system.file("tests", "test.bw", package = "rtracklayer") xx = import(test_bw, which=seqinfo(BigWigFile(test_bw))["chr19"]) > xx GRanges with 4 ranges and 1 metadata column: seqnames ranges strand | score <rle> <iranges> <rle> | <numeric> [1] chr19 [1501, 1800] * | 0.25 [2] chr19 [1801, 2100] * | 0.5 [3] chr19 [2101, 2400] * | 0.75 [4] chr19 [2401, 2700] * | 1 --- seqlengths: chr2 chr19 243199373 59128983 Martin > -------------------------------------- > Dario Strbenac > PhD Student > University of Sydney > Camperdown NSW 2050 > Australia > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793