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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
