[Bioc-sig-seq] rtracklayer and import()ing into GRanges

[Patrick Aboyoun]

Michael,
How integrated would you like to see the GRanges class in rtracklayer? 
The rtracklayer::GenomicData constructor is the master instantiator. I 
would like to add an asRangedData = TRUE (default) argument to the 
GenomicData function and push it all the way up through the import 
functions where when the user sets asRangedData = FALSE, the GenomicData 
function would create a GRanges object. This is what we did with the 
{matchPWM,vmatchPattern,vmatchPDict},BSgenome-methods in the BSgenome 
package and it as good a solution as any. This is a straight-forward 
change and wouldn't take too long to complete.


Patrick


On 8/4/10 12:56 PM, Michael Lawrence wrote:
> GRanges support is definitely on the TODO list. Filters are a good idea and
> also on the TODO list, possibly with a chunk size parameter to enable chunk
> processing.
>
> I'd love to have the GRanges stuff at least done by the next release.
> Patches welcome, of course :)
>
> Michael
>
> On Wed, Aug 4, 2010 at 8:08 AM, Ivan Gregoretti<ivangreg at gmail.com>  wrote:
>
>    
>> Hello Michael and everyone,
>>
>> Would you please consider adding to import() the capacity to generate
>> a GRanges object rather than the default RangedData object?
>>
>> Also,
>>
>> Wouldn't it be great to be able to import() with filters just like
>> with readAligned()?
>>
>>
>>
>> Justification
>>
>> GRanges is a biology-aware container. When importing large BEDs into
>> R, the current workflow involves creating RangedData first and then
>> converting to GRanges.
>>
>> If the BEDs are really big, holding both objects in memory at any
>> point in time is a hardware challenge.
>>
>> The capacity to filter the input would help in this case and in
>> general it would provide an increase in efficiency.
>>
>>
>> Thank you,
>>
>> Ivan
>>
>>
>>
>>
>> Ivan Gregoretti, PhD
>> National Institute of Diabetes and Digestive and Kidney Diseases
>> National Institutes of Health
>> 5 Memorial Dr, Building 5, Room 205.
>> Bethesda, MD 20892. USA.
>> Phone: 1-301-496-1016 and 1-301-496-1592
>> Fax: 1-301-496-9878
>>
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>> Bioc-sig-sequencing at r-project.org
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>>
>>      
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