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@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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>

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