[Bioc-devel] [devteam-bioc] Very slow when operate GRangesList

Hi,

SimpleLists are slow in this situation, basically because the underlying
seqselect is slow, due to this loop:

             x <- do.call(c, lapply(seq_len(length(ir)), function(i)
window(x,
                 start = start(ir)[i], width = width(ir)[i])))

Am I missing something or could this become a simple x[as.integer(ir)]?

In the meantime, using CompressedLists is the way to go. So for an
RleList, you need to pass compress=TRUE to the constructor.


On Wed, Aug 21, 2013 at 8:30 AM, Ou, Jianhong <Jianhong.Ou at umassmed.edu
<mailto:Jianhong.Ou at umassmed.edu>> wrote:

    Hi,

    When I use big set of GrangesList, I found it become very slow when
    metadata contain AtomicList. e.g.

     > grll <- GRanges(seqnames="chr1", ranges=IRanges(start=1:500,

    width=2), someInfo=rep(RleList("*"), 500))

     > grr <- split(grll, 1:500)
     > grl <- as.list(grr)
     > system.time(grl<- grl[500:1])

        user  system elapsed
           0       0       0

     > system.time(grr<- grr[500:1])

        user  system elapsed
       1.622   0.013   1.635

     > grll <- GRanges(seqnames="chr1", ranges=IRanges(start=1:500,

    width=2))

     > grr <- split(grll, 1:500)
     > grl <- as.list(grr)
     > system.time(grl<- grl[500:1])

        user  system elapsed
           0       0       0

     > system.time(grr<- grr[500:1])

        user  system elapsed
       0.029   0.001   0.030

     > sessionInfo()

    R Under development (unstable) (2013-07-23 r63392)
    Platform: x86_64-apple-darwin12.4.0 (64-bit)

    locale:
    [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

    attached base packages:
    [1] parallel  stats     graphics  grDevices utils     datasets
      methods   base

    other attached packages:
    [1] GenomicRanges_1.13.36 XVector_0.1.0         IRanges_1.19.24
       BiocGenerics_0.7.3

    loaded via a namespace (and not attached):
    [1] stats4_3.1.0 tools_3.1.0

    Is there any method to improve this?

    Yours sincerely,

    Jianhong Ou

    LRB 670A
    Program in Gene Function and Expression
    364 Plantation Street Worcester,
    MA 01605

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