Non overlapping granges (or opposite of subsetByOverlaps)

Question: Non overlapping granges (or opposite of subsetByOverlaps)

4.2 years ago by

India

vinod.acear • 40 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

iranges genomicranges granges subsetbyoverlaps • 4.1k views

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modified 12 months ago by doublehelix31 • 0 • written 4.2 years ago by vinod.acear • 40

Answer: Non overlapping granges (or opposite of subsetByOverlaps)

4.2 years ago by

Steve Lianoglou ♦ 12k

Denali

Steve Lianoglou ♦ 12k 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

ADD COMMENT • link written 4.2 years ago by Steve Lianoglou ♦ 12k

Thanks Steve , it worked

ADD REPLY • link written 4.2 years ago by vinod.acear • 40

Thanks Steve , it worked

ADD REPLY • link written 4.2 years ago by vinod.acear • 40

Thanks Steve , it worked

ADD REPLY • link written 4.2 years ago by vinod.acear • 40

Thanks Steve , it worked

ADD REPLY • link written 4.2 years ago by vinod.acear • 40

Answer: Non overlapping granges (or opposite of subsetByOverlaps)

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.

ADD COMMENT • link written 4.2 years ago by Hervé Pagès ♦♦ 14k

Answer: Non overlapping granges (or opposite of subsetByOverlaps)

12 months ago by

doublehelix31 • 0

Germany, Freiburg, University of Freiburg

doublehelix31 • 0 wrote:

subsetByOverlaps(gr1, gr2, invert = TRUE)

does it.

ADD COMMENT • link modified 12 months ago • written 12 months ago by doublehelix31 • 0

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