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

[Ivan Gregoretti]

Hi Patrick,

Since the upgrade yesterday morning, this problem seems to have gone
away. That is good news, I guess.

I'll report to the list if I bump into it again.

Thank you very much for trying to solve the problem.

Ivan

Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health



On Mon, Apr 26, 2010 at 4:42 PM, Patrick Aboyoun <paboyoun at fhcrc.org> wrote:
> 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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>>
>
>