[BioC] Genomic Ranges. Ignore strandedness in findOverlap function.

[Steve Lianoglou]

Hi Fahim,


On Fri, Jan 6, 2012 at 4:08 PM, Fahim Mohammad <fahim.md at 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