Error running table() on an RleList returned by coverage()
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Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 4 days ago
CRUK, Cambridge, UK

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

 

 
GenomicRanges S4Vectors • 881 views
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@herve-pages-1542
Last seen 3 days ago
Seattle, WA, United States

Hi Rory,

I fixed that bug yesterday in IRanges 1.99.31 but the fix won't propagate to the public repos until tomorrow. In the mean time you can get IRanges 1.99.31 directly from svn:

  svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges

user: readonly, password: readonly

Cheers,

H.

 

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Excellent, thanks Hervé!

-Rory

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