Retrieving overlaps inside a single dataset using foverlaps

Question

[startup_biostar]

1 chr1 58710367 58719391

2 chr1 58710476 58716325

Got a data as above in a single dataset. How to use foverlaps to perform Union ?

This should return 1 chr1 58710367 58719391.

How would I do that?

if it was

1 chr1 58710367 58719391

2 chr1 58719390 58719999

This should return 1 chr1 58710367 58719999

Answer 1

[Amirosein]

you can use reduce() to perform union, for example we first make a GRanges object with your coordinates:

sep = GRanges( seqnames = "chr1", ranges = IRanges(start=c(58710367,58710476),end=c(58719391, 58716325)), strand = "+")

resulting:

GRanges object with 2 ranges and 0 metadata columns:
  seqnames               ranges strand
     <Rle>            <IRanges>  <Rle>
[1]     chr1 [58710367, 58719391]      +
[2]     chr1 [58710476, 58716325]      +

and then using reduce() to perform union:

U = reduce( sep )

resulting:

GRanges object with 1 range and 0 metadata columns:
  seqnames               ranges strand
     <Rle>            <IRanges>  <Rle>
[1]     chr1 [58710367, 58719391]      +

Remember that this function is sensitive to strand direction and won't union intervals from "+" and "-" strands, but if strand sets to "*" it works