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Question: Non overlapping granges (or opposite of subsetByOverlaps)
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gravatar for vinod.acear
3.0 years ago by
vinod.acear • 20
India
vinod.acear • 20 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
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modified 3.0 years ago by Hervé Pagès ♦♦ 13k • written 3.0 years ago by vinod.acear • 20
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gravatar for Steve Lianoglou
3.0 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 3.0 years ago by Steve Lianoglou ♦ 12k

Thanks Steve ,  it worked

ADD REPLY • link written 3.0 years ago by vinod.acear • 20

Thanks Steve ,  it worked

ADD REPLY • link written 3.0 years ago by vinod.acear • 20

Thanks Steve ,  it worked

ADD REPLY • link written 3.0 years ago by vinod.acear • 20

Thanks Steve ,  it worked

ADD REPLY • link written 3.0 years ago by vinod.acear • 20
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gravatar for Hervé Pagès
3.0 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k 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.
ADD COMMENT • link written 3.0 years ago by Hervé Pagès ♦♦ 13k
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