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...@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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>
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>
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