[BioC] BigWig Import by Chromosome

[Martin Morgan]

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
>
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