[BioC] IRanges problem: findOverlaps

[Nicolas Delhomme]

Hi all,

I'm not sure about intervals, but genomeIntervals is chromosome-aware (http://bioconductor.org/packages/release/bioc/html/genomeIntervals.html). The syntax is as described by Alex, since genomeIntervals extends intervals.

Whether you use genomeIntervals or IRanges is just a matter of taste, really.

Cheer,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------





On Jul 10, 2012, at 6:34 PM, Ivan Gregoretti wrote:

> Hi Alex,
> 
> I am not sure interval_overlap() is better option than findOverlaps().
> 
> Is interval_overlap() aware that intervals may lie in different chromosomes?
> 
> In other words, every peak has three coordinates: chromosome, start
> and end. The findOverlaps() function is aware of that.
> 
> Thank you,
> 
> Ivan
> 
> 
> Ivan Gregoretti, PhD
> 
> 
> On Tue, Jul 10, 2012 at 12:05 PM, alessandro brozzi
> <alessandro.brozzi at gmail.com> wrote:
>> hi Nicolas,
>> 
>> I don't know very well Iranges but to find overlapping intervals the
>> package "intervals"
>> 
>> http://cran.fhcrc.org/web/packages/intervals/index.html
>> 
>> is very straightforward.
>> 
>> Here an example:
>> 
>> peaks  =  matrix(
>>                           c(
>>                              2,  8,
>>                              8,  9,
>>                              6,  9,
>>                             11, 12,
>>                              3,  3
>>                             ),
>>                           ncol = 2, byrow = TRUE
>>                           )
>> 
>>> peaks
>>     [,1] [,2]
>> [1,]    2    8
>> [2,]    8    9
>> [3,]    6    9
>> [4,]   11   12
>> [5,]    3    3
>>> 
>> 
>> track =  matrix(
>>                           c(
>>                             2,  8,
>>                             3,  4,
>>                             5, 10
>>                             ),
>>                           ncol = 2, byrow = TRUE
>>                           )
>> 
>> track
>>     [,1] [,2]
>> [1,]    2    8
>> [2,]    3    4
>> [3,]    5   10
>> 
>> interval_overlap ( Intervals(peaks), Intervals(track))
>> 
>> [[1]]
>> [1] 1 2 3
>> 
>> [[2]]
>> [1] 1 3
>> 
>> [[3]]
>> [1] 1 3
>> 
>> [[4]]
>> integer(0)
>> 
>> [[5]]
>> [1] 1 2
>> 
>> the result is a list: for each peak you have the indexes of the
>> corresponding overlapping items of the track matrix. Setting some options
>> you can fine tune your research.
>> 
>> HTH,
>> Alex
>> 
>> 
>> On Tue, Jul 10, 2012 at 5:40 PM, Nicolas DESCOSTES <
>> descostes at ciml.univ-mrs.fr> wrote:
>> 
>>> Dear members,
>>> 
>>> I have a set of chip-Seq peaks which I want to find the overlap with a
>>> bench of annotations downloaded from ucsc.
>>> 
>>> When I am doing the overlap between my peaks and annotations list, I am
>>> finding 5635 positive matches. When adding "type = "start"", I have no
>>> results returned. However, when I am visualizing the 5635 intervals, it
>>> overlaps many start site of my genes annotations.
>>> 
>>> I tried to update IRanges but I am still getting no results.
>>> 
>>> Any idea?
>>> 
>>> Thanks.
>>> 
>>> 
>>>        [[alternative HTML version deleted]]
>>> 
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>> 
>>        [[alternative HTML version deleted]]
>> 
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> 
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