Hi Michael,
Martin and I have been discussing this. In addition to the fix you
suggest, what do you think of changing the default to compressed=TRUE
for the RleList constructor? Rle is the only one of the AtomicLists with
default FALSE. Was there a reason for this when it was first implemented?
Val
On 08/22/2013 07:34 PM, Maintainer wrote:
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
<mailto: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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