find overlapping genomic coordinates in more than two datasets

Question

I want to compare and get the overlapping regions in three different dataset. The comparison should also be based on the CNA.

 data1
      chr start         end       CNA
        1   170900001   171500001   loss
        1   11840001    19420001    loss
        1   60300001    62700001    gain
        1   25520001    25820001    gain

data2
    chr  start       end        CNA
    1   170940001   171500001   gain
    1   60300001    62700001    gain
    1   25520001    25840001    gain
    1   119860001   123040001   loss
    1   171500001   171580001   gain
    1   79240001    84420001    gain


data 3
chr  start       end        CNA
1   170950001   171500001   gain
1   60300001    62700001    loss
1   25530001    25840001    gain

expected output

   chr  start       end        CNA
    1   170950001   171500001   gain
    1   25530001    25840001    gain

I used GenomicRanges for the comparison. First i tried to sort the genomic regions based on the "gain" and "loss". Then i used findOverlaps between each group separately for eg. df1 <- findOverlaps(data1,data2) and then findOverlaps(df1,data3). I know there are options bed tools but would be great to know if there is any alternative methods in getting the desired output using GenomicRanges?

If you're looking for expert help with GenomicRanges, please consider asking your question instead on the [Bioconductor support site](https://support.bioconductor.org). I think the answer is just what I think you are doing -- `findOverlaps()` for data1 and data2, then the result of that and data3. — Martin Morgan, Apr 15 '15 at 18:57
Does [this SO answer](http://stackoverflow.com/questions/23331475/r-overlap-multiple-granges-with-findoverlaps) solve your problem? — eipi10, Apr 15 '15 at 19:09

score 0 · Answer 1 · edited May 23 '17 at 11:50

0

I did ask a similar question several days ago. You don't mention whether GenomicRanges worked for you or not. I found that the library IRange did work much better for me. Maybe my approach can be useful for you

edited May 23 '17 at 11:50

Community

1
1

answered Apr 15 '15 at 20:46

Antonio Rodriguez Franco

150
6

i tried with GenomicRanges intersect, which worked fine for me. – beginner Apr 15 '15 at 22:18

find overlapping genomic coordinates in more than two datasets

1 Answers1