[Bioc-sig-seq] coverage() is misbehaving with (apparently sound) GRanges object

[Patrick Aboyoun]

Ivan,
I can't reproduce this. Could you provide an example?

Thanks,
Patrick


On 4/23/10 2:28 PM, Ivan Gregoretti wrote:
> Hi all,
>
> coverage(), naughty boy!
>
> I have two GRanges instances
>
> # my 100 million tags
>    
>> class(B)
>>      
> [1] "GRanges"
> attr(,"package")
> [1] "GenomicRanges"
>
> # a few ChIP-seq peaks
>    
>> class(P)
>>      
> [1] "GRanges"
> attr(,"package")
> [1] "GenomicRanges"
>
> # Now I want to keep only the tags in-peak
>    
>> BP<- B[B %in% P,]
>>      
> # Are you ok BP?
>    
>> class(BP)
>>      
> [1] "GRanges"
> attr(,"package")
> [1] "GenomicRanges"
> # Good.
>
> # Now, whilst coverage(B) and coverage(P) work, BP crashes
>    
>> coverage(BP)
>>      
> Error in coverage.normargWidth(width, length(x)) :
>    'x' has no element and 'width' is NULL
>
>
> BP is, I understand, I subset of B. Why would it crash coverage()?
>
>
> Thank you,
>
> Ivan
>
>    
>> sessionInfo()
>>      
> R version 2.12.0 Under development (unstable) (2010-03-25 r51410)
> x86_64-unknown-linux-gnu
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8
>   [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=C
> LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> LC_ADDRESS=C
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] BSgenome.Mmusculus.UCSC.mm9_1.3.16 chipseq_0.3.5
>   [3] ShortRead_1.5.21                   lattice_0.18-3
>   [5] BSgenome_1.15.19                   Biostrings_2.15.25
>   [7] GenomicRanges_0.0.9                IRanges_1.5.70
>   [9] rtracklayer_1.7.11                 RCurl_1.3-1
> [11] bitops_1.0-4.1
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.6.1 grid_2.12.0   hwriter_1.1   tools_2.12.0  XML_2.6-0
>
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