On Mon, Oct 19, 2009 at 10:25 AM, Chris Seidel <seidel@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.
>
>
This is the normal behavior of apply functions in R. The additional
arguments are passed in whole to the function every time it is invoked. We
don't have an "mapply" variant of gdapply, so you'll need to do some extra
work, like keeping track of an index.

Perhaps we could make this easier using metadata? We know the genome of
'extendedReads' so 'coverage' could be smart and refer to the appropriate
BSgenome package.

Michael



> -Chris
>
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