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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