[Bioc-sig-seq] countOverlaps Help

Dario Strbenac D.Strbenac at garvan.org.au
Wed Jan 27 23:38:14 CET 2010

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 ?


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