[BioC] Bug in GenomicRanges precede/follow

[Valerie Obenchain]

Hi Aaron,

Thanks for catching this. Now fixed in GenomicRanges 1.8.8 in release 
and 1.9.35 in devel.

Valerie


On 07/18/2012 10:17 PM, a.statham at garvan.org.au wrote:
> Hi,
>
> I just ran into this bug using the GRanges method of nearest
> (which calls precede&  follow) with ignore.strand=TRUE
>
>> nearest(GRanges("chr1", IRanges(1, width=1)),
> GRanges("chr1", IRanges(10, width=1)), ignore.strand=TRUE)
> Error in strand(x)<- strand(subject)<- "+" : object 'x' not
> found
>
>
> And tracked it down to here
>
>> GenomicRanges:::.findPrecedeFollow_GRanges
> function (query, subject, select, ignore.strand, where =
> c("precede",
>      "follow"))
> {
>      leftOf<- "precede" == match.arg(where)
>      if (ignore.strand)
>          strand(x)<- strand(subject)<- "+"
>
> strand(x) should be strand(query)
>
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> 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=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
>   [1] xtable_1.7-0
> BSgenome.Hsapiens.UCSC.hg19_1.3.17
>   [3] BSgenome_1.24.0                    Biostrings_2.24.1
>   [5] multicore_0.1-7                    rtracklayer_1.16.3
>   [7] Repitools_1.2.0                    GenomicRanges_1.8.7
>   [9] IRanges_1.14.4                     BiocGenerics_0.2.0
> [11] limma_3.12.1
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-4.1  RCurl_1.91-1    Rsamtools_1.8.5
> stats4_2.15.0
> [5] tcltk_2.15.0    tools_2.15.0    XML_3.9-4
> zlibbioc_1.2.0
>
>
> Thanks,
> Aaron
>
> ---
> Aaron Statham
> Postgraduate Scholar, Cancer Epigenetics
> Garvan Institute of Medical Research   Tel: (02) 9295 8386
> 384 Victoria St Darlinghurst 2010   Fax: (02) 9825 8316
> NSW Australia         email: a.statham at garvan.org.au
>
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