Merge overlapping ranges into unique groups, in dataframe

Question

I have a dataframe of n rows and 3

df <- data.frame(start=c(178,400,983,1932,33653),
    end=c(5025,5025, 5535, 6918, 38197),
    group=c(1,1,2,2,3))

df         


        

Answer 1

You'll need IRanges package:

require(IRanges)
ir <- IRanges(df$start, df$end)
df$group2 <- subjectHits(findOverlaps(ir, reduce(ir)))
> df

#  start   end group group2
# 1   178  5025     1      1
# 2   400  5025     1      1
# 3   983  5535     2      1
# 4  1932  6918     2      1
# 5 33653 38197     3      2

To install IRanges, type these lines in R:

source("http://bioconductor.org/biocLite.R")
biocLite("IRanges")

To learn more (manual etc..) go here