Hi there, I'm using findOverlaps on GRanges objects and am playing with the select options. It looks like only two of the four options described in the help page are implemented for GRanges objects, whereas for RangedData all four options are available. The code below should say it all (I think). Would it be possible to implement those at some point? It seems like they're useful options (and the less coercing back and forth between GRanges and RangedData I have to do, the happier I will be). thanks, Janet > library(GenomicRanges) Loading required package: IRanges Attaching package: ?IRanges? The following object(s) are masked from ?package:base?: cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, setdiff, table, union > > gr <- GRanges(seqnames=Rle(c('Chrom1', 'Chrom2', 'Chrom3'), c(3, 3, 4)), + IRanges(1:10, width=5)) > > findOverlaps(gr, gr, select="first") [1] 1 1 1 4 4 4 7 7 7 7 > findOverlaps(gr, gr, select="all") An object of class "RangesMatching" Slot "matchMatrix": query subject [1,] 1 1 [2,] 1 2 [3,] 1 3 [4,] 2 1 ### etc > findOverlaps(gr, gr, select="last") Error in match.arg(select) : 'arg' should be one of ?all?, ?first? > findOverlaps(gr, gr, select="arbitrary") Error in match.arg(select) : 'arg' should be one of ?all?, ?first? > > findOverlaps(as(gr,"RangedData"), as(gr,"RangedData"), select="arbitrary") CompressedIntegerList of length 3 [["Chrom1"]] 1 1 1 [["Chrom2"]] 1 1 1 [["Chrom3"]] 1 1 1 1 > findOverlaps(as(gr,"RangedData"), as(gr,"RangedData"), select="last") CompressedIntegerList of length 3 [["Chrom1"]] 3 3 3 [["Chrom2"]] 3 3 3 [["Chrom3"]] 4 4 4 4 > > > sessionInfo() R version 2.14.0 (2011-10-31) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicRanges_1.6.4 IRanges_1.12.4 > >