[R] fusion of overlapping intervals

[Martin Morgan]

On 11/05/2012 09:14 AM, Hermann Norpois wrote:
> Hello,
>
> I have start and end coordinates from different experiments (DNase
> hypersensitivity data) and now I would like to combine overlapping
> intervals. For instance (see my test data below) (2) 30-52 and (3) 49-101
> are combined to 30-101. But 49-101 and 70-103 would not be combined because
> they are on different chromosomes (chr a and chr b).
> Does anybody have an idea?

This data is very naturally handled by the "GRange" class  in Bioconductor's 
GenomicRanges package

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

   gr = GRanges(rep(c("a", "b"), each=3),
                IRanges(c(5, 30, 49, 70, 100, 129),
                        c(10, 52, 101, 103, 130, 140)),
                strand="*")

and then

 > reduce(gr)
GRanges with 3 ranges and 0 metadata columns:
       seqnames    ranges strand
          <Rle> <IRanges>  <Rle>
   [1]        a [ 5,  10]      *
   [2]        a [30, 101]      *
   [3]        b [70, 140]      *
   ---
   seqlengths:
     a  b
    NA NA

There are vignettes

   vignette(package="GenomicRanges")

and additional training material, e.g.,

   http://bioconductor.org/help/course-materials/2012/CSC2012/

If you pursue this solution then please follow-up with questions on the 
Bioconductor mailing list

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

Martin

> Thanks
> Hermann
>
>> df
>    chr start end
> 1   a     5  10
> 2   a    30  52
> 3   a    49 101
> 4   b    70  103
> 5   b   100 130
> 6   b   129 140
>> dput (df)
> structure(list(chr = structure(c(1L, 1L, 1L, 2L, 2L, 2L), .Label = c("a",
> "b"), class = "factor"), start = c(5, 30, 49, 70, 100, 129),
>      end = c(10, 52, 101, 103, 130, 140)), .Names = c("chr", "start",
> "end"), row.names = c(NA, -6L), class = "data.frame")
>
> 	[[alternative HTML version deleted]]
>
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