Finding overlap in dataframe ranges in R - r

Question

I have two bedfiles as dataframes in R, for which I want to map all overlapping regions to each other (similar to what bedtools closest would be able to do).
BedA:
chr start end
2 100 500
2 200 250
3 275 300
BedB:
chr start end
2 210 265
2 99 106
8 275 290
BedOut:
chr start.A end.A start.B end.B
2 100 500 210 265
2 100 500 99 106
2 200 250 210 265
Now, I found this very similar question, which suggest to use iRanges. Using the proposed way seems works, but I have no idea how to turn the output into a data frame like "BedOut".

Answer 1

Another data.table option using foverlaps:
setkeyv(BedA, names(BedA))
setkeyv(BedB, names(BedB))
ans <- foverlaps(BedB, BedA, nomatch=0L)
setnames(ans, c("start","end","i.start","i.end"), c("start.A","end.A","start.B","end.B"))
output:
chr start.A end.A start.B end.B
1: 2 100 500 99 106
2: 2 100 500 210 265
3: 2 200 250 210 265
data:
library(data.table)
BedA <- fread("chr start end
2 100 500
2 200 250
3 275 300")
BedB <- fread("chr start end
2 210 265
2 99 106
8 275 290")

Answer 2

Here is a solution using the data.table package.
library(data.table)
chr = c(2,2,3)
start.A = c(100, 200, 275)
end.A = c(500, 250, 300)
df_A = data.table(chr, start.A, end.A)
chr = c(2,2,8)
start.B = c(210, 99, 275)
end.B = c(265, 106, 290)
df_B = data.table(chr, start.B, end.B)
First, inner join the data-tables on the key chr:
df_out = df_B[df_A, on="chr", nomatch=0]
Then filter the overlapping interval:
df_out = df_out[(start.A>=start.B & start.A<=end.B) | (start.B>=start.A & start.B<=end.A)]
setcolorder(df_out, c("chr", "start.A", "end.A", "start.B", "end.B"))
chr start.A end.A start.B end.B
1: 2 100 500 210 265
2: 2 100 500 99 106
3: 2 200 250 210 265