In the genomic ranges package for R, is there an option in
setdiff that prevents the collapsing of adjacent ranges? for example, If I have the following:
gr1 = GRanges object  chr1 1-10 *  chr1 11-20 *  chr1 21-30 * gr2 = GRanges object  chr1 18-25 *
and I take
What I get:
setdiff( gr1, gr2 )  chr1 1-17 * # <-- 1-10 and 11-20 are reduced together automatically; I don't want this.  chr1 26-30 *
The output stops at 17 and picks up again at 26 to avoid gr2 from 18-25, so at least that much is correct, but unfortunately, my output now has a single continuous range from 1 to 17 instead of 1-10, and a different GRange directly adjacent from 11-17. There's a reduce operation being done automatically that I want to suppress.
What I want:
setdiff( gr1, gr2, <Some_option_to_suppress_reduce> )  chr1 1-10 *  chr1 11-17 *  chr1 26-30 *
I don’t want these first two regions to be reduced into one.
What I've tried:
The best solution I've come up with so far is to convert to a list and then back to GRange, like this:
unlist( GRangesList( lapply( 1:length(gr1), function(i) setdiff ( gr1[i], gr2) ) ))
..which does what I want but with all the converting between data types it's really slow and inefficient. Is there an option to turn off reduce directly (or some other more elegant solution)?