overlapping intervals in a dataframe in r

Question

I am trying to work on genomic data with R, and I have seen a couple of topics with quite good answers related to two dataframes and overlapping intervals. My problem is that I have one dataframe with overlapping intervals, which I would like to merge, i.e:

chrom   start   stop
 5       100     105
 5       100     105
 5       200     300
 9       275     300
 9       280     301

I would like to end up with something like this:

chrom   start   stop
 5       100     105
 5       200     300
 9       275     301

I am also trying to become better at coding, so I was wondering what would be the most elegant way to do it. Hope this is not redundant with some other query,

Answer 1

Using GenomicRanges::reduce:

require(GenomicRanges)
as.data.frame(reduce(GRanges(df$chrom, IRanges(df$start, df$stop))))
#   seqnames start end width strand
# 1        5   100 105     6      *
# 2        5   200 300   101      *
# 3        9   275 301    27      *

It's also possible using data.table::foverlaps or GenomicRanges::findOverlaps, but not as straightforward.