[Bioc-sig-seq] findOverlaps with GenomicRanges?

[Janet Young]

Hi,

Thanks, Martin - that'll work.

I also just realized that for RangedData, findOverlaps is correctly assuming subject=query when I only specify one set of ranges as input.  But for GenomicRanges, it doesn't have that default set up.  If I specify subject as well:
	findOverlaps(myregions_GR, myregions_GR) 
then findOverlaps DOES work for GenomicRanges.

On top of that, I want to use the argument 
	ignoreSelf=T
which works combined with your workaround (adding type="any") but not mine (specifying both subject and query).

thanks again,

Janet




On Feb 22, 2011, at 8:43 PM, Martin Morgan wrote:

> 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
>> 
>> _______________________________________________ Bioc-sig-sequencing
>> mailing list Bioc-sig-sequencing at r-project.org 
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> 
> 
> -- 
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> 
> Location: M1-B861
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