Question

Non overlapping granges (or opposite of subsetByOverlaps)

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vinod.acear ▴ 50

@vinodacear-8884

Last seen 4.3 years ago

India

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

granges genomicranges iranges subsetByOverlaps • 9.7k views

ADD COMMENT • link updated 2.8 years ago by b.simpson • 0 • written 9.2 years ago by vinod.acear ▴ 50

score 2 · Answer 1 · 2015-09-27

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 21 months ago

United States

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 9.2 years ago Steve Lianoglou ★ 13k

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Thanks Steve , it worked

ADD REPLY • link 9.2 years ago vinod.acear ▴ 50

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Thanks Steve , it worked

ADD REPLY • link 9.2 years ago vinod.acear ▴ 50

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Thanks Steve , it worked

ADD REPLY • link 9.2 years ago vinod.acear ▴ 50

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Thanks Steve , it worked

ADD REPLY • link 9.2 years ago vinod.acear ▴ 50

score 2 · Answer 2 · 2018-12-07

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doublehelix31 ▴ 20

@doublehelix31-18729

Last seen 6.0 years ago

Germany, Freiburg, University of Freibu…

subsetByOverlaps(gr1, gr2, invert = TRUE)

does it.

ADD COMMENT • link 6.0 years ago doublehelix31 ▴ 20

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subsetByOverlaps(gr1, gr2, invert = TRUE), is the better option if you want to keep your metadata columns!

ADD REPLY • link 2.8 years ago b.simpson • 0

score 1 · Answer 3 · 2015-09-30

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Hervé Pagès 16k

@herve-pages-1542

Last seen 9 hours ago

Seattle, WA, United States

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.

ADD COMMENT • link 9.2 years ago Hervé Pagès 16k