Finding overlapping ranges between two interval data

Question

I have one table with coordinates (start, end) of ca. 500000 fragments and another table with 60000 single coordinates that I would like to match w

Answer 1

Does this work? You can use merge first and then subset

   kk<-merge(dtFrags,dtCoords,by="chr",all.x=TRUE)
> kk
   chr id.x start end   type id.y coord
1:   1    1   100 200   exon   10   150
2:   2    2   300 500 intron   20   300
3:   2    4   250 600   exon   20   300
4:   X    3   400 600 intron   NA    NA


 kk[coord>=start & coord<=end]
   chr id.x start end type id.y coord
1:   1    1   100 200 exon   10   150
2:   2    4   250 600 exon   20   300

Answer 2

In general, it's very appropriate to use the bioconductor package IRanges to deal with problems related to intervals. It does so efficiently by implementing interval tree. GenomicRanges is another package that builds on top of IRanges, specifically for handling, well, "Genomic Ranges".

require(GenomicRanges)
gr1 = with(dtFrags, GRanges(Rle(factor(chr, 
          levels=c("1", "2", "X", "Y"))), IRanges(start, end)))
gr2 = with(dtCoords, GRanges(Rle(factor(chr, 
          levels=c("1", "2", "X", "Y"))), IRanges(coord, coord)))
olaps = findOverlaps(gr2, gr1)
dtCoords[, grp := seq_len(nrow(dtCoords))]
dtFrags[subjectHits(olaps), grp := queryHits(olaps)]
setkey(dtCoords, grp)
setkey(dtFrags, grp)
dtFrags[, list(grp, id, type)][dtCoords]

   grp id   type id.1 chr coord
1:   1  1   exon   10   1   150
2:   2  2 intron   20   2   300
3:   2  4   exon   20   2   300
4:   3 NA     NA   30   Y   500