[R] Intersection of two chromosomal ranges

[Martin Morgan]

On 03/04/2012 11:06 AM, Yadav Sapkota wrote:
> Hi,
>
> I want to merge multiple chromosomal regions based on their common
> intersecting regions. I tried couple of things using while and if loops but
> did not work out.
>
> I would appreciate if anyone could provide me a small piece of code in R to
> get the intersection of following example:
>
> chr1: 100-150
> chr1: 79-250
> chr1: 100-175
> chr1: 300-350
>
> I want the intersection of all four regions as follow:
> chr1: 100-150
> chr1: 300-350
>
> I have thousands of these regions (some overlap and some not).

Not exactly sure what you mean by 'intersection of all four regions' but

   source("http://bioconductor.org/biocLite.R")
   biocLite("GenomicRanges")

and then

   library(GenomicRanges)
   q = GRanges("chr1", IRanges(c(100,  79, 100, 300),
                               c(150, 250, 175, 350)))
   s = GRanges("chr1", IRanges(c(100, 300),
                               c(150, 350)))
   o = findOverlaps(query=q, subject=s)
   xtabs(~queryHits(o) + subjectHits(o))

leading to
             subjectHits(o)
queryHits(o) 1 2
            1 1 0
            2 1 0
            3 1 0
            4 0 1

This will be efficient for (10's of) millions of overlaps. There are 
extensive vignettes for help, vignettes(package="IRanges"), 
vignettes(package="GenomicRanges") and the Bioconductor mailing list

   http://bioconductor.org/help/mailing-list/

is the appropriate place for further help in this direction.

Martin

>
> Regards,
> --Yadav
>
> 	[[alternative HTML version deleted]]
>
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