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

[Peter Hickey]

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

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