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

[Nicolas Delhomme]

Hej Michael, Hervé!

I have to admit that I’m not exactly following the details of your discussion here. What would appear intuitive for me for a findOverlaps function on GRangesList, GRangesList is that it returns a list of findOverlaps on GRanges,GRanges. I can see difficulties in determining the concordance between the GRanges of the two GRangesList though. And I don’t have the overview to decide whether such a behaviour would be consistent, but that’s naively what I would expect.

Anyway, just my 2 cts. Thanks for taking a look.

Cheers,

Nico

---------------------------------------------------------------
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 19:43, Michael Lawrence <lawrence.michael at gene.com> wrote:

> 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 at 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 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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> >
> 
>