[BioC] findOverlaps method in GenomicRanges not supporting type="equal" for GRangesList, GRangesList?

[Nicolas Delhomme]

Thanks!
---------------------------------------------------------------
Nicolas Delhomme

Nathaniel Street Lab
Department of Plant Physiology
Umeå Plant Science Center

Tel: +46 90 786 7989
Email: nicolas.delhomme at plantphys.umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
---------------------------------------------------------------

On 21 Nov 2013, at 17:06, Michael Lawrence <lawrence.michael at gene.com> wrote:

> I will work on this today.
> 
> Michael
> 
> 
> On Thu, Nov 21, 2013 at 4:43 AM, Nicolas Delhomme <nicolas.delhomme at umu.se> wrote:
> Hej Bioc!
> 
> When I try to find “equal” ranges from two GRangesList object, I get the following error:
> 
> > findOverlaps(query=grng.def,subject=grng.mod,type="equal")
> Error in match.arg(type) :
>   'arg' should be one of “any”, “start”, “end”, “within”
> 
> Isn’t type=“equal” supported for the GRangesList, GRangesList signature?
> 
> Cheers,
> 
> Nico
> 
> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin13.0.0 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
>  [1] easyRNASeq_1.8.2       ShortRead_1.20.0       Rsamtools_1.14.1       GenomicRanges_1.14.3   DESeq_1.14.0           lattice_0.20-24        locfit_1.5-9.1
>  [8] Biostrings_2.30.1      XVector_0.2.0          IRanges_1.20.5         edgeR_3.4.0            limma_3.18.3           biomaRt_2.18.0         Biobase_2.22.0
> [15] genomeIntervals_1.18.0 BiocGenerics_0.8.0     intervals_0.14.0
> 
> loaded via a namespace (and not attached):
>  [1] annotate_1.40.0      AnnotationDbi_1.24.0 bitops_1.0-6         DBI_0.2-7            genefilter_1.44.0    geneplotter_1.40.0   grid_3.0.2           hwriter_1.3
>  [9] latticeExtra_0.6-26  LSD_2.5              RColorBrewer_1.0-5   RCurl_1.95-4.1       RSQLite_0.11.4       splines_3.0.2        stats4_3.0.2         survival_2.37-4
> [17] tools_3.0.2          XML_3.98-1.1         xtable_1.7-1         zlibbioc_1.8.0
> 
> 
> ---------------------------------------------------------------
> Nicolas Delhomme
> 
> Nathaniel Street Lab
> Department of Plant Physiology
> Umeå Plant Science Center
> 
> Tel: +46 90 786 7989
> Email: nicolas.delhomme at plantphys.umu.se
> SLU - Umeå universitet
> Umeå S-901 87 Sweden
> 
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