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.
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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
