Thanks Hervé!
________________________________________
From: Hervé Pagès [hpa...@fhcrc.org]
Sent: 06 October 2014 21:48
To: Rory Stark; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Error running table() on an RleList returned by
coverage()
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]]
>
> _______________________________________________
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>
--
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
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