[Bioc-sig-seq] Coverage for RangeList?

[Jane Landolin]

Hi all,

I just joined the list, and was hoping to get some advice about the
best way to work with the various classes that deal with genomic range
info. I am a postdoc in the Celniker Lab at Lawrence Berkeley National
Lab, working on the modENCODE project.

So my question has to do with using various functions that operate on
the IRanges level, while keeping my data in RangedData or RangeList
objects.  I should be able to use rdapply or lapply, but it is not
very clear to me when I should use one over another.

If I want to calculate the chromosome-by-chromosome coverage for a
RangeData object, I can do something like:

lapply(ranges(RangedData),coverage, start = 1, end = 1000)

but how can I do it for varying starts and ends?

Alternatively, is it better to write a function and call it using
rdapply?  What have you guys been doing for this scenario?


Thanks in advance,
Jane Landolin