On Wed, Jan 27, 2010 at 2:38 PM, Dario Strbenac <D.Strbenac@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 ?
>
>
This one is easy -- the countOverlaps() method really does not exist for
RangesList. I just added it to devel. In the meantime, you can use
sum(queryRangesList %in% SubjRangesList) to get the same answer.

Hope that helps,
Michael

Thanks,
>       Dario.
>
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