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

[Hervé Pagès]

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}}