Hi Rory, See my answer on the support site about this (posted this morning). Thanks,
H. On 10/06/2014 01:46 PM, Rory Stark wrote:
I posted this earlier on the main support site, but I realize I should have posted it here. Our package build is breaking on a call to table() with the results of a call to coverage(). We pass in a GRanges and get back a RleList. This used to work. Easiest way to reproduce is using the example from the GenomicRanges::coverage man page: gr <- GRanges( seqnames=Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)), ranges=IRanges(1:10, end=10), strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)), seqlengths=c(chr1=11, chr2=12, chr3=13)) cvg <- coverage(gr) What used to happen:table(cvg)0 1 2 3 4 chr1 1 4 1 5 0 chr2 3 1 1 7 0 chr3 9 1 1 1 1 What happens now:table(cvg)Error in as.vector(x, mode) : invalid 'mode' argument Can anyone help? I see that GenomicRanges is broken right now in the development build, perhaps this will be fixed when that is... Cheers- Rory [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
