Dear all,

would appreciate your help with a simple question :

I am working with a set of GRanges : eg : (chr1: 100 - 200) and  (chr1: 200 - 300)

and 

I would like to get the OVERLAP/ INTERSECTION only the GRanges within a special interval :

eg : (chr1 : 0 - 250), in an INCLUSIVE WAY,

namely only the interval (chr1: 100 - 200), that is completely included in the region (chr1 : 0 - 250) ..

is there any function in GRanges I could quickly use in this regard ? thank you and happy weekend !

-- bogdan

Hi Bogdan,

gr <- GRanges("chr1", IRanges(c(100, 200), c(200, 300)))
my_region <- GRanges("chr1", IRanges(0, 250))
gr %within% my_region
## [1]  TRUE FALSE

Note that %within% is just a shortcut for:

overlapsAny(gr, my_region, type="within")
## [1]  TRUE FALSE

See ?findOverlaps for more information.

H.

HI Herve, thank you very much !