[Bioc-devel] Changes to Hits class in devel branch affecting distanceToNearest method

[Peter Hickey]

Thanks, Val and Herve.
On 08/11/2014, at 8:47 AM, Valerie Obenchain <vobencha at fredhutch.org> wrote:

> These issues are fixed in IRanges 2.1.8 and GenomicRanges 1.19.5.
> 
> Valerie
> 
> 
> On 11/05/14 18:32, Hervé Pagès wrote:
>> Hi Peter,
>> 
>> The new validity method for Hits revealed some issues with
>> the behavior of "distanceToNearest" method for GRanges objects.
>> The major issue being that it sometimes returns a Hits
>> object with NAs in it. Val will address this in the next few
>> days.
>> 
>> Cheers,
>> H.
>> 
>> 
>> On 11/05/2014 06:21 PM, Peter Hickey wrote:
>>> This message may be a bit premature or redundant since after writing
>>> it I now see that Herve is in the midst of work on the Hits class in
>>> S4Vectors.
>>> 
>>> My package GenomicTuples is currently failing R CMD check in the devel
>>> branch
>>> (http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicTuples/zin2-checksrc.html).
>>> I tracked down the error to a problem with my
>>> distanceToNearest,GTuples,GTuples-method. However, this is simply
>>> defined via inheritance to the
>>> distanceToNearest,GenomicRanges,GenomicRanges-method and so I believe
>>> the problem lies with the
>>> distanceToNearest,GenomicRanges,GenomicRanges-method.
>>> 
>>> The following example adapted from nearest-methods {GenomicRanges}
>>> docs demonstrates the change in behaviour between the release and
>>> devel branch. It appears to be due to a new validity check of the Hits
>>> object returned by distanceToNearest. As I said, I now see that Herve
>>> recently started some work on the Hits class in S4Vectors, which
>>> includes this validity check, so this is really just a heads up that
>>> these changes affect the distanceToNearest method, in case this hasn't
>>> already been noted.
>>> 
>>> Thanks,
>>> Pete
>>> 
>>> #---------------------------------------------------------------------------------------------------
>>> 
>>> # BioC release
>>>>   library(GenomicRanges)
>>>>   query <- GRanges(c("A", "B"), IRanges(c(1, 5), width=1))
>>>>   subject <- GRanges("A", IRanges(c(6, 5, 13), c(10, 10, 15)))
>>>>   distanceToNearest(query, subject)
>>> Hits of length 2
>>> queryLength: 2
>>> subjectLength: 3
>>>   queryHits subjectHits  distance
>>>    <integer>   <integer> <integer>
>>>  1         1           2         3
>>>  2         2          NA        NA
>>>> sessionInfo()
>>> R version 3.1.1 (2014-07-10)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>> 
>>> locale:
>>>  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
>>>  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
>>>  [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8
>>>  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
>>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>>> 
>>> attached base packages:
>>> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
>>> [8] methods   base
>>> 
>>> other attached packages:
>>> [1] GenomicRanges_1.18.1 GenomeInfoDb_1.2.2   IRanges_2.0.0
>>> [4] S4Vectors_0.4.0      BiocGenerics_0.12.0
>>> 
>>> loaded via a namespace (and not attached):
>>> [1] XVector_0.6.0
>>> #---------------------------------------------------------------------------------------------------
>>> 
>>> 
>>> #---------------------------------------------------------------------------------------------------
>>> 
>>> # BioC devel
>>>>   library(GenomicRanges)
>>>> query <- GRanges(c("A", "B"), IRanges(c(1, 5), width=1))
>>>> subject <- GRanges("A", IRanges(c(6, 5, 13), c(10, 10, 15)))
>>>> distanceToNearest(query, subject)
>>> Error in validObject(.Object) :
>>>   invalid class “Hits” object: 'subjectHits(x)' must contain non-NA
>>> values >= 1 and <= 'subjectLength(x)'
>>>> sessionInfo()
>>> R Under development (unstable) (2014-10-29 r66891)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>> 
>>> locale:
>>>  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
>>>  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
>>>  [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8
>>>  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
>>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>>> 
>>> attached base packages:
>>> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
>>> [8] methods   base
>>> 
>>> other attached packages:
>>> [1] GenomicRanges_1.19.4 GenomeInfoDb_1.3.6   IRanges_2.1.5
>>> [4] S4Vectors_0.5.3      BiocGenerics_0.13.0
>>> 
>>> loaded via a namespace (and not attached):
>>> [1] XVector_0.7.1
>>> #---------------------------------------------------------------------------------------------------
>>> 
>>> 
>>> --------------------------------
>>> Peter Hickey,
>>> PhD Student/Research Assistant,
>>> Bioinformatics Division,
>>> Walter and Eliza Hall Institute of Medical Research,
>>> 1G Royal Parade, Parkville, Vic 3052, Australia.
>>> Ph: +613 9345 2324
>>> 
>>> hickey at wehi.edu.au
>>> http://www.wehi.edu.au
>>> 
>>> ______________________________________________________________________
>>> The information in this email is confidential and inte...{{dropped:19}}
>> 
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
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> 

--------------------------------
Peter Hickey,
PhD Student/Research Assistant,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
Ph: +613 9345 2324

hickey at wehi.edu.au
http://www.wehi.edu.au


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