On Mon, Apr 19, 2010 at 4:40 PM, Jane Landolin <landolin@gmail.com> wrote:

> 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)
>
>
Many Ranges methods are defined on RangedData and RangesList. coverage() is
one of these. Note that 'shift' and 'width' are the parameters to be used
instead of 'start' and 'end'. They can be vectors in the case of
RangedData/RangesList, with an element for each element of those structures
(i.e. an element for each chromosome).


> 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
>
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