[BioC] IRanges: Trying to cut overlapping intervals into pieces

Elizabeth Purdom epurdom at stat.berkeley.edu
Sat Jan 24 07:24:57 CET 2009


I am trying to take overlapping intervals and return a set of intervals 
that are not overlapping but cover all of the region (and mantain the 
intervals that don't overlap). In particular, I don't want to merge 
intervals that overlap together (i.e. the reduce function in IRanges)-- 
I want to cut them up into distinct regions. For example, if I have 
[1,6], [4,8], [7,10]
I want to get back the set of adjacent intervals:
The options I find that look like they perhaps do this (intersect or 
setdiff?) seem to be related to the 'normal' ranges class; but this 
class requires a gap between intervals -- no adjacent intervals -- which 
is not what I want. Is there a nice way to do this with IRanges (or a 
not so nice one, but fast)?

Similarly, is there a 'reduce' version that doesn't merge adjacent 
intervals but only truly overlapping ones? There are a lot of annotation 
examples where you wouldn't not want to merge adjacent intervals (e.g. UTRs)

Thanks for any assistance!
Elizabeth Purdom
Division of Biostatistics
UC, Berkeley

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