Yes that requires the development version of IRanges. Sorry for not specifying that. Michael On Fri, Feb 20, 2009 at 10:51 PM, Elizabeth Purdom < epurdom@stat.berkeley.edu> wrote: > Do I need a development version to have the function 'ranges' defined for > the output of overlap? I get an error when I try to do this myself. > Thanks, > Elizabeth > > > > isContained<-function(a,b){#a,b, ranges > + require(IRanges) > + ol<-overlap(a,b) > + m<-as.matrix(ol) > + contained<-m[width(ranges(ol)) == width(b[m[,1]]),] > + return(contained) > + } > > a<-IRanges(c(1,2,3),c(4,5,6)) > > b<-IRanges(c(1,2,3),c(3,6,6)) > > isContained(a,b) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "ranges", for signature > "RangesMatching" > Error in width(ranges(ol)) : > error in evaluating the argument 'x' in selecting a method for function > 'width' > > sessionInfo() > R version 2.8.1 (2008-12-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] IRanges_1.0.11 > > loaded via a namespace (and not attached): > [1] grid_2.8.1 lattice_0.17-17 Matrix_0.999375-17 tools_2.8.1 > > > > > Michael Lawrence wrote: > >> How about this: >> >> Find ranges in 'b' completely contained within ranges in 'a': >> >> ol <- overlap(a, b) >> m <- as.matrix(ol) >> contained <- m[width(ranges(ol)) == width(b[m[,1]]),] >> >> So 'contained' is the overlap matrix, filtered by whether the intersection >> of the overlap (ranges(ol)) has the same width as the query range. >> >> On Fri, Feb 20, 2009 at 4:53 PM, Elizabeth Purdom < >> epurdom@stat.berkeley.edu <mailto:epurdom@stat.berkeley.edu>> wrote: >> >> Hi, >> I'm very happy with the efficiency of the overlap function and I was >> wondering if there is a fast way in IRanges to find which of the >> ranges in one set are completely contained by one or more ranges in >> another set (i.e. the same idea as overlap, but more restrictive >> criteria than any overlap)? I don't want to assume anything about my >> two set of ranges (e.g. that they are 'normal'). >> Thanks very much, >> Elizabeth Purdom >> UC, Berkeley >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch <mailto:bioconductor@stat.math.ethz.ch> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> [[alternative HTML version deleted]]