I wish I could patch it myself and share it. Unfortunately, my R proficiency does not descent to such a low programming level.
Please let us know when you get the chance to work on it. I bet that there are quite a few users that are interested. Thank you, Ivan On Wed, Aug 4, 2010 at 3:56 PM, Michael Lawrence <[email protected]> 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 >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
