Thanks Steve.
I resolved the problem. Actually I was using ignore.strand option with
RangedData object.
Thanks again.
Fahim


On Fri, Jan 6, 2012 at 4:41 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi Fahim,
>
>
> On Fri, Jan 6, 2012 at 4:08 PM, Fahim Mohammad <fahim.md@gmail.com> wrote:
> > Hi
> > findOverlap function depends on the 'strand'edness of the subject and
> > query. In the example below, I am using findOverlap function to find
> > overlapping ranges.  Is there a way to completely ignore this feature and
> > report all overlaps.
>
> [snip]
>
> Do this in your R workspace:
>
> R> library(GenomicRanges)
> R> getMethod('findOverlaps', c("GenomicRanges", "GenomicRanges"))
>
> And notice that the findOverlaps method when called on GenomicRanges
> objects has an `ignore.strand` argument that you can set to TRUE to
> get what you are want, so, do:
>
> R> o <- findOverlaps(grQuery, grSubject, ignore.strand=TRUE)
>
> HTH,
> -steve
>
> > grSubject <-
> >  GRanges(
> > seqnames =Rle(rep("chr1", 7)),
> > ranges = IRanges(c(1,5,15,22,5,15,22),c(11,8,20,30,8,17,25)),
> > strand = Rle(strand(c("-", rep("+",6)))),
> > name = c('a', 'b','b','b','c','c','c')
> > )
> >> grSubject
> > GRanges with 7 ranges and 1 elementMetadata value:
> >      seqnames    ranges strand |        name
> >         <Rle> <IRanges>  <Rle> | <character>
> >  [1]     chr1  [ 1, 11]      - |           a
> >  [2]     chr1  [ 5,  8]      + |           b
> >  [3]     chr1  [15, 20]      + |           b
> >  [4]     chr1  [22, 30]      + |           b
> >  [5]     chr1  [ 5,  8]      + |           c
> >  [6]     chr1  [15, 17]      + |           c
> >  [7]     chr1  [22, 25]      + |           c
> >  ---
> >  seqlengths:
> >   chr1
> >     NA
> >
> >
> > grQuery <-
> >  GRanges(
> > seqnames =Rle(rep("chr1", 3)),
> > ranges = IRanges(c(6,14,22),c(10,16,27)),
> > strand = Rle(strand(rep("-",3))),
> > name = c('x', 'y','z')
> > )
> >> grQuery
> > GRanges with 3 ranges and 1 elementMetadata value:
> >      seqnames    ranges strand |        name
> >         <Rle> <IRanges>  <Rle> | <character>
> >  [1]     chr1  [ 6, 10]      - |           x
> >  [2]     chr1  [14, 16]      - |           y
> >  [3]     chr1  [22, 27]      - |           z
> >  ---
> >  seqlengths:
> >   chr1
> >     NA
> >
> > as.matrix(findOverlaps(grQuery, grSubject))
> >  query subject
> > [1,]     1       1
> >
> >
> > When I change the strand of the query like this:
> > grQuery <-
> > GRanges(
> > seqnames =Rle(rep("chr1", 3)),
> > ranges = IRanges(c(6,14,22),c(10,16,27)),
> > strand = Rle(strand(c("-", rep("+",2)))),
> > name = c('x', 'y','z')
> > )
> >
> > I get
> >> as.matrix(findOverlaps(grQuery, grSubject))
> >     query subject
> > [1,]     1       1
> > [2,]     2       3
> > [3,]     2       6
> > [4,]     3       4
> > [5,]     3       7
> >>
> >
> >
> > Thanks
> >
> > Fahim
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
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>
>
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>

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