Merge some rows into one when the data is continuous - r

Question

I have a bed file which is loaded as a dataframe into R. Genomic coordinates that looks something likes this:
chrom start end
chrX 400 600
chrX 800 1000
chrX 1000 1200
chrX 1200 1400
chrX 1600 1800
chrX 2000 2200
chrX 2200 2400
There's no need to keep all the rows and it would be nicer to compact it to something like this:
chrom start end
chrX 400 600
chrX 800 1400
chrX 1600 1800
chrX 2000 2400
How can I possibly do it?
I've tried to think of something with dplyr but no success. group_by wouldn't work because I don't know how to modify chunks of continuous rows into one using start coordinate from the first row and end coordinate from the last row also because there are many of these chunks.

Answer 1

Using GenomicRanges package from bioconductor, built specifically for bed files and the like:
library(GenomicRanges)
# Example data
gr <- GRanges(
seqnames = Rle("chr1", 6),
ranges = IRanges(start = c(400 ,800, 1200, 1400, 1800, 2000),
end = c(600, 1000, 1400, 1600, 2000, 2200)))
gr
# GRanges object with 6 ranges and 0 metadata columns:
# seqnames ranges strand
# <Rle> <IRanges> <Rle>
# [1] chr1 [ 400, 600] *
# [2] chr1 [ 800, 1000] *
# [3] chr1 [1200, 1400] *
# [4] chr1 [1400, 1600] *
# [5] chr1 [1800, 2000] *
# [6] chr1 [2000, 2200] *
# -------
# seqinfo: 1 sequence from an unspecified genome; no seqlengths
# merge contiouse ranges into one using reduce:
reduce(gr)
# GRanges object with 4 ranges and 0 metadata columns:
# seqnames ranges strand
# <Rle> <IRanges> <Rle>
# [1] chr1 [ 400, 600] *
# [2] chr1 [ 800, 1000] *
# [3] chr1 [1200, 1600] *
# [4] chr1 [1800, 2200] *
# -------
# seqinfo: 1 sequence from an unspecified genome; no seqlength
# EDIT: if the bed file is a data.frame we can convert it to ranges object:
gr <- GRanges(seqnames(Rle(df$chrom),
ranges = IRanges(start = df$start,
end = df$end)))