[Bioc-sig-seq] findOverlaps with GenomicRanges?

[Martin Morgan]

On 02/22/2011 09:04 PM, Janet Young wrote:
> 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.

Hi Janet --

not sure what you mean. I have

gr = GRanges(seqnames=c("chr1","chr1","chr2"),
             ranges=IRanges(start=c(101L,201L,101L),
                            end=c(250L,301L,201L)))
identical(findOverlaps(gr, type="any"),
          findOverlaps(gr, gr, type="any"))

maybe you were just indicating the workaround findOverlaps(gr, gr)?

> 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).

ignoreSelf is only available for a signature like
findOverlaps,RangedData,missing, or findOverlaps,GRanges,missing, so
asking to ignore self with 2 arguments never works. From ?findOverlaps

          If 'subject' is omitted, 'query' is queried against itself.
          In this case, and only this case, the 'ignoreSelf' and
          'ignoreRedundant' arguments are allowed. By default, the

Better to expend the keystrokes and type TRUE rather than T

> T <- FALSE # surprises ahead!
> TRUE <- FALSE
Error in TRUE <- FALSE : invalid (do_set) left-hand side to assignment

'T' is a plain old variable, TRUE a language reserved words.

Martin

> 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
>> Telephone: 206 667-2793
> 


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793