On Mon, Oct 19, 2009 at 10:25 AM, Chris Seidel <[email protected]> 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 > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
