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
[email protected]
http://www.wehi.edu.au
______________________________________________________________________
The information in this email is confidential and inte...{{dropped:19}}
_______________________________________________
[email protected] mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
