I have 2 GRanges objects (gr1,gr2). I want to find partial overlaps between them, that is I want to find which ranges in gr2 overlap the i th range in gr1 but are not entirely contained in it (its fine if gr1[i] is entirely contained in some of those gr2 ranges).

I thought I can use findOverlaps once with type='any' and once with type='within',

something along these lines:

overlapsAny<-as.data.frame(findOverlaps(query=gr2,subject=gr1,type='any'))

overlapsFull<-as.data.frame(findOverlaps(query=gr2,subject=gr1,type='within'))

overlapsAny$Combination<-apply(overlapsAny,1,function(row) paste(row$queryHits,row$subjectHits,sep='.'))

overlapsFull$combination<-apply(overlapsFull,1,function(row) paste(row$queryHits,row$subjectHits,sep='.'))

partial<-!(which(overlapsAny$Combination%in%overlapsFull$combination)

Is there a less convoluted way to do this (such as directly intersecting hits objects somehow)?

Thanks in adavnce

Dolev Rahat

You should avoid coercing the Hits objects to data.frames, because that discards the semantics and all conveniences gained from them. 

Just do something like:

anyHits <- findOverlaps(gr2, gr1)
withinHits <- findOverlaps(gr2, gr1, type="within")
setdiff(anyHits, withinHits)

These classes exist to make your life easier, not harder. The obvious thing usually works.