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
>>
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>>
>>
>>

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