[Bioc-sig-seq] findOverlaps with GenomicRanges?

[Martin Morgan]

On 02/22/2011 08:22 PM, Janet Young wrote:
> Hi there,
> 
> Is findOverlaps supposed to work on GRanges objects?  For me it works
> on RangedData but not on GRanges - see below for the error,
> sessionInfo, etc.   It would be useful for me if it could also work
> on GRanges, so if this doesn't count as a bug report can we count it
> as a feature request?

Hi Janet -- it's a bug; try

> ??findOverlaps
> ?"findOverlaps,GenomicRanges,GenomicRanges-method"
> findOverlaps(myregions_GR, type="any")
An object of class "RangesMatching"
Slot "matchMatrix":
     query subject
[1,]     1       1
[2,]     1       2
[3,]     2       1
[4,]     2       2
[5,]     3       3

Slot "DIM":
[1] 3 3

or another appropriate argument for 'type'. It seems to be fixed in devel.

Martin


> 
> thanks very much,
> 
> Janet
> 
> 
> -------------------------------------------------------------------
> 
> Dr. Janet Young (Trask lab)
> 
> Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N.,
> C3-168, P.O. Box 19024, Seattle, WA 98109-1024, USA.
> 
> tel: (206) 667 1471 fax: (206) 667 6524 email: jayoung  ...at...
> fhcrc.org
> 
> http://www.fhcrc.org/labs/trask/
> 
> -------------------------------------------------------------------
> 
> 
> 
>> library(GenomicRanges)
> Loading required package: IRanges
> 
> Attaching package: 'IRanges'
> 
> The following object(s) are masked from 'package:base':
> 
> cbind, eval, Map, mapply, order, paste, pmax, pmax.int, pmin, 
> pmin.int, rbind, rep.int, table
> 
>> 
>> myregions_GR <-
>> GRanges(seqnames=c("chr1","chr1","chr2"),ranges=IRanges(start=c(101L,201L,101L),end=c(250L,301L,201L))
>> )
>> 
>> findOverlaps(myregions_GR)
> Error in match.arg(type) : 'arg' must be of length 1
>> 
>> 
>> myregions_RD <-
>> RangedData(IRanges(start=c(101L,201L,101L),end=c(250L,301L,201L)),space=c("chr1","chr1","chr2"),strand=c("+","+","+")
>> )
>> 
>> findOverlaps(myregions_RD)
> RangesMatchingList of length 2 names(2): chr1 chr2
>> 
>> sessionInfo()
> R version 2.12.1 (2010-12-16) Platform: x86_64-unknown-linux-gnu
> (64-bit)
> 
> locale: [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C [3]
> LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C
> LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C [11]
> LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages: [1] stats     graphics  grDevices utils
> datasets  methods   base
> 
> other attached packages: [1] GenomicRanges_1.2.3 IRanges_1.8.9
> 
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