Thanks, Val and Herve. On 08/11/2014, at 8:47 AM, Valerie Obenchain <[email protected]> wrote:
> 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 >>> >>> [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 > -------------------------------- 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 intend...{{dropped:8}}
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