[BioC] How to convert from IRanges(List) to Rle(List)

[Nicolas Delhomme]

Hi Martin,

I had to change my data structure, but using transcriptLocs2refLocs, computation time is down to one second!!!

Amazing, really. Thanks!!

Nico

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------





On 7 Apr 2012, at 20:12, Martin Morgan wrote:

> On 04/07/2012 05:39 AM, Nicolas Delhomme wrote:
>> Hi all,
>> 
>> I'm just wondering if there would be a direct way to convert an
>> IRanges to an Rle, as in: as(rng,"Rle"). At the moment, I can convert
>> my IRanges into an integer vector and cast that as an Rle
>> (Rle(as.integer(rng)), but that is not extremely efficient on a long
>> IRangesList (with>  700,000 IRanges in it). Takes ~10 mins with an
>> sapply.
>> 
>> Why I want that is for the following: I have an IRangesList of
>> transcripts (describing exons at the genome level) and for every one,
>> I have a bp position at the transcript level that I want to convert
>> into a genomic bp position. Basically, I need to be able to convert a
>> given transcript coordinate into the corresponding genomic
>> coordinate. My IRanges contain the genomic coordinates of every
>> transcript and by converting it into an integer vector, I can select
>> the right genomic bp coordinate by using the transcript bp coordinate
>> as an index (as.integer(rng)[transcript.pos]).
>> 
>> I considered the IRanges approach because I keep the transcript name
>> and I'm sure that I looking up the right coord in the right
>> transcript, but I'm open to other suggestions.
> 
> Hi Nico -- VariantAnnotation::refLocsToLocalLocs, GenomicFeatures::transcriptLocs2refLocs and IRanges::map might do this for you; no direct experience on my part, though. Martin
> 
>> 
>> Thanks for any pointers,
>> 
>> Cheers,
>> 
>> Nico
>> 
>> ---------------------------------------------------------------
>> Nicolas Delhomme
>> 
>> Genome Biology Computational Support
>> 
>> European Molecular Biology Laboratory
>> 
>> Tel: +49 6221 387 8310 Email: nicolas.delhomme at embl.de
>> Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany
>> 
>> _______________________________________________ Bioconductor mailing
>> list Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the
>> archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 
> -- 
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> 
> Location: M1-B861
> Telephone: 206 667-2793