On Fri, Jul 24, 2009 at 7:47 AM, Johannes Waage <johannes.waage@bric.dk>wrote:

> Hi all,
>
> In assigning RNA-seq data to exon-models, I'm looking for a proper overlap
> function. Both IRanges and genomeIntervals have overlap functions, but as
> far as I can see, these don't have options for contained overlaps, example:
>
>
> |-------Range 1-------]
>     [----Range 2----]
>
> IRanges, genomeIntervals: TRUE
> Wanted: TRUE
>
>
> |-------Range 1-------]
>                 [----Range 2----]
>
>
> IRanges, genomeIntervals: TRUE
> Wanted: FALSE
>
> Any suggestions are appreciated!
>

It's fairly easy to filter the overlaps for this condition. To find where an
entire query range (in b) overlaps a subject range (in a):

ol <- overlap(a, b)
width(ranges(ol, a, b)) == width(b)

Is this what you wanted?

Michael



>
> Regards,
> Johannes Waage,
> Uni. of Copenhagen
>
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