Question: Non overlapping granges (or opposite of subsetByOverlaps)
0
4.2 years ago by
vinod.acear40
India
vinod.acear40 wrote:

I have two granges (gr1 and gr2)  in which all ranges of gr2 overlaps with ranges of gr1. How can i find granges of gr1 that are not overlaping with gr2?  i.e.  black color output given on the link http://bedops.readthedocs.org/en/latest/_images/reference_setops_bedops_difference_ab@2x.png

modified 12 months ago by doublehelix310 • written 4.2 years ago by vinod.acear40
Answer: Non overlapping granges (or opposite of subsetByOverlaps)
2
4.2 years ago by
Denali
Steve Lianoglou12k wrote:

I believe "setdiff" should do what you want. Browse through this intro vignette for more info: http://www.bioconductor.org/packages/release/bioc/vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.pdf

Thanks Steve ,  it worked

Thanks Steve ,  it worked

Thanks Steve ,  it worked

Thanks Steve ,  it worked

Answer: Non overlapping granges (or opposite of subsetByOverlaps)
1
4.2 years ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:

Hi,

FWIW subsetByOverlaps(gr1, gr2) is equivalent to gr1[gr1 %over% gr2] so you would get the opposite with gr1[!(gr1 %over% gr2)]. This is not what you seem to want though: you seem to want setdiff() (thanks Steve). Just wanted to clarify the difference.

H.

Answer: Non overlapping granges (or opposite of subsetByOverlaps)
0
12 months ago by
Germany, Freiburg, University of Freiburg
doublehelix310 wrote:

subsetByOverlaps(gr1, gr2, invert = TRUE)

does it.