Question

how to extract Granges not overlapping with other ganges?

1

Entering edit mode

vinod.acear ▴ 50

@vinodacear-8884

Last seen 5.2 years ago

India

Hi

i Have two granges (gr1 and gr2) and i want to extract granges from gr2 that are not overlapping with gr1. Please tell me the possible way to do it

Granges findoverlaps • 5.5k views

ADD COMMENT • link updated 10.0 years ago by James W. MacDonald 68k • written 10.0 years ago by vinod.acear ▴ 50

1

Entering edit mode

Note that you already asked this 5 weeks ago here Non overlapping granges (or opposite of subsetByOverlaps) and got the same answer.

H.

ADD REPLY • link 10.0 years ago Hervé Pagès 16k

score 6 · Accepted Answer · 2015-11-03

6

Entering edit mode

James W. MacDonald 68k

@james-w-macdonald-5106

Last seen 1 day ago

United States

> gr1 <- GRanges("chr1", IRanges(c(1,3,5), c(8,9,15)))
> gr2 <- GRanges("chr1", IRanges(c(1,3,5,17), c(8,9,17,35)))
> gr2[!gr2 %over% gr1,]
GRanges object with 1 range and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1  [17, 35]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

ADD COMMENT • link 10.0 years ago James W. MacDonald 68k

1

Entering edit mode

Also can use %outside% here instead of negating %over%.

ADD REPLY • link 10.0 years ago Michael Lawrence ★ 11k