I guess the documentation for ?findOverlaps needs to be clarified. "start" and "end" mean that two ranges would need to have the exact same start or end, respectively, for there to be a hit. Does that help? I hope you don't mind that I've cc'd the bioconductor list. Michael On Fri, Jun 20, 2014 at 8:53 AM, khauser <khauser130d@gmail.com> wrote: > Dear Dr. Lawrence, > > I have been using the IRanges package specifically the findOverlaps > function. I have read the help files for the type="start", type="end" and > type="all" arguments but I'm still unclear as to the differences. > > When I have tried this out on my data I get, for example, 900,000 hits for > the type="all" data but only ~30,000 for the type="start" and type="end" > data. I would have thought based on my reading that the sum of type="start" > and type="end" would give the total for type="all". Clearly I'm > misunderstanding. Is there some visual depiction of these different types > of overlap? > > Many thanks, > Kaleb > [[alternative HTML version deleted]]