Using findOverlaps to find only partial overlaps
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d r ▴ 150
@d-r-5459
Last seen 4.2 years ago
Israel

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

findoverlaps genomicranges • 857 views
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Entering edit mode
@michael-lawrence-3846
Last seen 5 months ago
United States

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.

 
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