[Bioc-sig-seq] countOverlaps Help

[Vincent Carey]

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
<D.Strbenac at garvan.org.au> 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.
>
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