Finding overlap in ranges with R

Question

I have two data.frames each with three columns: chrom, start & stop, let\'s call them rangesA and rangesB. For each row of rangesA, I\'m looking to find which (if any)

Answer 1

For your example data:

rangesA <- data.frame(
    chrom = c(5, 1, 9),
    start = c(100, 200, 275),
    stop = c(105, 250, 300)
)
rangesB <- data.frame(
    chrom = c(1, 5, 9),
    start = c(200, 99, 275),
    stop = c(265, 106, 290)
)

This will do it with sapply, such that each column is one row in rangesA and each row is corresponding row in rangesB:

> sapply(rangesA$stop, '>=', rangesB$start) & sapply(rangesA$start, '<=', rangesB$stop)
      [,1]  [,2]  [,3]
[1,] FALSE  TRUE FALSE
[2,]  TRUE FALSE FALSE
[3,] FALSE FALSE  TRUE