[Bioc-sig-seq] gdapply, coverage, and widths for all chromosomes

[Deepayan Sarkar]

On Mon, Oct 19, 2009 at 10:25 AM, Chris Seidel <seidel at phaget4.org> wrote:
> In using gdapply to get coverage over all chromosomes of a
> GenomeDataList object:
>
> cov <- gdapply(extendedReads, coverage)
>
> how do you supply the "width" argument to coverage? When I try handing
> it a vector of chromosome lengths, it complains that it needs a single
> value.

You cannot. That's a limitation of gdapply, potentially fixable by
making the chromosome lengths available as phenodata associated with
the "GenomeDataList" object.

One reason for not addressing this limitation yet is that for most
downstream operations the default choice of 'width' seemed OK. Could
you explain why that is not sufficient in your case?

-Deepayan