So I've checked into devel a match,GRangesList,GRangesList. This allows
findMatches() to return what you want. There is a question though before
this is approved: does it make sense for match() to act like findOverlaps
and consider each GRanges atomically (one returned index per GRanges) or
should match behave as it does other Lists and return an IntegerList, with
a value per range, grouped by the top-level elements. If we decide on the
latter, then the method I wrote needs to be removed and the implementation
moved to the "equals" mode in findOverlaps. Either way,
findOverlaps(type="equals") should be made to work.

Michael


On Thu, Nov 21, 2013 at 8:13 AM, Nicolas Delhomme
<nicolas.delhomme@umu.se>wrote:

> Thanks!
> ---------------------------------------------------------------
> Nicolas Delhomme
>
> Nathaniel Street Lab
> Department of Plant Physiology
> Umeå Plant Science Center
>
> Tel: +46 90 786 7989
> Email: nicolas.delhomme@plantphys.umu.se
> SLU - Umeå universitet
> Umeå S-901 87 Sweden
> ---------------------------------------------------------------
>
> On 21 Nov 2013, at 17:06, Michael Lawrence <lawrence.michael@gene.com>
> wrote:
>
> > I will work on this today.
> >
> > Michael
> >
> >
> > On Thu, Nov 21, 2013 at 4:43 AM, Nicolas Delhomme <
> nicolas.delhomme@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@plantphys.umu.se
> > SLU - Umeå universitet
> > Umeå S-901 87 Sweden
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
>

	[[alternative HTML version deleted]]

