[BioC] Faster way to apply a function than endoapply on 40K GrangesList

[Martin Morgan]

On 08/10/2011 12:36 PM, Lakshmanan Iyer wrote:
> Hi,
> I am trying to add 10K to the end of the intervals in a GRangesList
> object using endoapply and flank using the comand:
> p3UTRs10K<- endoapply(p3UTRs,function (z) flank (z, 10000,start=FALSE));

maybe along the lines of

   example(GRangesList)
   ranges(grl) = flank(ranges(grl), 10000, start=FALSE)

which gives

 > end(grl)
CompressedIntegerList of length 3
[["gr1"]] 6
[["gr2"]] 9 15
[["gr3"]] 3 9
 > ranges(grl) = flank(ranges(grl), 1000, start=FALSE)
 > start(grl)
CompressedIntegerList of length 3
[["gr1"]] 7
[["gr2"]] 10 16
[["gr3"]] 4 10
 > end(grl)
CompressedIntegerList of length 3
[["gr1"]] 1006
[["gr2"]] 1009 1015
[["gr3"]] 1003 1009

? Martin

>
> I am writing to find out if someone has a suggestion for a faster way
> of doing this?  With 40000 elements it is taking a long time..
>
> Here is what I am doing:
>
> class (p3UTRs)
> [1] "GRangesList"
> attr(,"package")
> [1] "GenomicRanges"
>
> length (p3UTRs)
> [1] 41053
>
> p3UTRs10K<- endoapply(p3UTRs,function (z) flank (z, 10000,start=FALSE));
>
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] BSgenome.Mmusculus.UCSC.mm9_1.3.17 GenomicFeatures_1.4.0
>   [3] leeBamViews_0.99.11                BSgenome_1.20.0
>   [5] Biobase_2.12.1                     Rsamtools_1.4.1
>   [7] Biostrings_2.20.0                  GenomicRanges_1.4.3
>   [9] IRanges_1.10.0                     rtracklayer_1.12.0
> [11] RCurl_1.5-0                        bitops_1.0-4.1
>
> loaded via a namespace (and not attached):
> [1] biomaRt_2.8.0 DBI_0.2-5     RSQLite_0.9-4 tools_2.13.0  XML_3.2-0
>>
>
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