Thanks, Michael. That was the tip I was looking for. For what it's worth, neither args (ranges) nor ?ranges led me to the answer you so quickly provided. I spent more than a little time looking. I am a little timid about this -- I thought I already knew how to obtain answers of this sort :} -- but how exactly could I have found out this on my own? If it is straightforward, I will offer you not only my thanks, but my apologies also. Regards, - Paul On Jun 8, 2009, at 12:50 PM, Michael Lawrence wrote: > The function is expecting the query ranges and subject ranges as the > second and third argument, respectively. Those ranges are not stored > within the matching object, so need to be provided again. > > ranges(overlap.12, range.2, range.1) > > This is actually documented in the man page.

On Mon, Jun 8, 2009 at 3:11 PM, Paul Shannon <pshannon@systemsbiology.org>wrote: > Thanks, Michael. That was the tip I was looking for. > > For what it's worth, neither > > args (ranges) > > nor > > ?ranges > > led me to the answer you so quickly provided. I spent more than a little > time looking. > > I am a little timid about this -- I thought I already knew how to obtain > answers of this sort :} -- but how exactly could I have found out this on my > own? If it is straightforward, I will offer you not only my thanks, but my > apologies also. > Well, this is a problem with S4 documentation. 'ranges' is a generic function, with many methods. ?ranges will only take you to the man page that documents the "generic", which for IRanges often means the man page for the first method defined on it (the RangedData page, in this case). Ideally, each generic would have some sort of man page listing each method on a generic. However, it's not really possible to write such a page, since additional methods can be defined by other packages. Thus, we could only document the methods provided by IRanges. One way to get documentation on methods is syntax like: method?ranges("RangesMatching") or ?ranges(matching). showMethods("ranges") shows which methods are defined. Note that the documentation in IRanges is organized by class, much like in Java, so this will just take you the RangesMatching class docs. Then you need to scroll/search through it to find the actual documentation of ranges(). Michael > Regards, > > - Paul > > > > On Jun 8, 2009, at 12:50 PM, Michael Lawrence wrote: > > The function is expecting the query ranges and subject ranges as the >> second and third argument, respectively. Those ranges are not stored within >> the matching object, so need to be provided again. >> >> ranges(overlap.12, range.2, range.1) >> >> This is actually documented in the man page. >> > > [[alternative HTML version deleted]]