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

[Hervé Pagès]

Hi,

Note that the "flank" method for GRanges objects is strand aware and
in this context "end" means "3' end". If that's not what you want,
just do something like

   start(grl) <- end(grl) + 1L
   end(grl) <- end(grl) + 10000L

and you are done.

But if you really want the "3' end", I can't think of an easy/efficient
way, unless you do something *highly* NOT recommended like accessing
directly a slot of your GRangesList object:

<NEVER DO THIS!>

   grl at unlistData <- flank(grl at unlistData, 10000, start=FALSE)

</NEVER DO THIS!>

Of course we should provide a "flank" method for GRangesList
objects that will do the above so the user doesn't need to use
a dangerous/forbidden trick ;-)

H.


On 11-08-10 02:48 PM, Martin Morgan wrote:
> 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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>
>


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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