it will be best if you follow the posting guide, though perhaps some folks will parse your code abstractly and find the error. i'd recommend that you reproducibly generate your error by working with the kinds of structures created through example(countOverlaps) and give us your sessionInfo() as noted in the posting guide.
On Wed, Jan 27, 2010 at 5:38 PM, Dario Strbenac <[email protected]> wrote: > Hi all, > > I can't seem to get countOverlaps to work and from the documentation I seem > to be doing it the right way. When I replace countOverlaps by findOverlaps, > the last code line in this example works though. > > ----------------------------------------- > subjRanges <- mapply(IRanges, start = split(subjRegions$start, > subjRegions$chr), end = split(subjRegions$end, SubjRegions$chr)) > SubjRangesList <- do.call(RangesList, SubjRanges) > queryRanges <- mapply(IRanges, start = split(queryTable$genoStart, > queryTable$genoName), end = split(queryTable$genoEnd, queryTable$genoName)) > queryRangesList <- do.call(RangesList, queryRanges) > > counts <- countOverlaps(queryRangesList, SubjRangesList) > # gives : Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "countOverlaps", for > signature "SimpleRangesList", "SimpleRangesList" > ----------------------------------------- > > What's really happening here ? > > Thanks, > Dario. > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
