Hi Patrick, Many thanks for your quick reply. Now that you mention it, it does make sense that the function should operate at the top level. I'm just too used to using these functions and getting "what I expect" on the first try... ;o) Cheers, Cei Patrick Aboyoun wrote: > Cei, > The Details section of the relevant man page for subsetByOverlaps > explains its functionality > > help("subsetByOverlaps,GRangesList,GRanges-method") > > In short the subsetByOverlaps function operates at the object's "top" > level, not the within-element level, as the "[" operator behaves for a > standard R list. So in the GRangesList, GRanges case, either you select > the list element as it appears in the original object or you drop it > entirely. > > I am glad to see that you have mentioned using the endoapply function, > because that is exactly what I would have recommended. > > endoapply(grl, subsetByOverlaps, gr3) > > If your use case, however, involves a GRangesList with over a hundred > elements, however, this may not be performant enough and I can provide > you with lower level code that will be much faster. If this is a common > use case, we could add a new function that works for > IRangesList,IRanges; GRangesList,GRanges; etc. pairings and avoids the > endoapply framework. > > > Patrick > > > > On 7/16/10 4:01 AM, Cei Abreu-Goodger wrote: >> Hello, >> >> I think I've found another bug. If you use subsetByOverlaps with a >> GRangesList as query, the full object is returned, instead of the >> subset that overlaps: >> >> library(GenomicRanges) >> gr1 <- GRanges(seqnames=c("a","b"),ranges=IRanges(c(1,11), c(5,15))) >> gr2 <- GRanges(seqnames=c("a","b"),ranges=IRanges(c(1,11), c(5,15))) >> gr3 <- GRanges(seqnames=c("a"),ranges=IRanges(1,5)) >> grl <- GRangesList(gr1,gr2) >> >> identical(grl,subsetByOverlaps(grl, gr3)) >> [1] TRUE >> >> To get the behavior that I was expecting, you can do: >> endoapply(grl, subsetByOverlaps, gr3) >> >> Cheers, >> >> Cei >> >> > sessionInfo() >> R version 2.11.0 (2010-04-22) >> i386-apple-darwin9.8.0 >> >> locale: >> [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] GenomicRanges_1.0.6 IRanges_1.6.8 Biobase_2.8.0 >> >> loaded via a namespace (and not attached): >> [1] tools_2.11.0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor