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

These issues are fixed in IRanges 2.1.8 and GenomicRanges 1.19.5.

Valerie


On 11/05/14 18:32, Herv? Pag?s 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