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

[Ivan Gregoretti]

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