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<[email protected]> 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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