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@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.
>
>
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