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

[Valerie Obenchain]

On 04/07/12 16:30, Michael Lawrence wrote:
> On Sat, Apr 7, 2012 at 11:12 AM, Martin Morgan<mtmorgan at fhcrc.org>  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
>>
>>
> Right. Right now, IRanges::map will take things from global to local
> (either into transcripts or reads, depending on the argument). This takes
> the place of "refLocsToLocalLocs". What "map" needs to support is the
> reverse. I think we could do this with either a new function. I am not sure
> if it should be called reverseMap though, because it's not clear which is
> forward and which is reverse. Maybe we need mapToGlobal and mapToLocal? Or
> maybe "absolute" and "relative" are better terms?
>
> Btw, we are working on an "easier to use" interface for the
> transcriptLocsToRefLocs function and that should be integrated with any
> refactoring/renaming.
I like the idea of the map generic and where it is going. I think the 
mapToGlobal and mapToLocal terms are more clear. Assuming in mapToGlobal 
the 'from' would be along the lines of cDNA-based, cds-based, or 
protein-based coordinates. In mapToLocal the 'from' would always be 
genomic-based coordinates. Yes?

Valerie

>
> Let's get a discussion going.
>
> Michael
>
>
>>> 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
>>>
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>>
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