# [SOLVED] How to remove overlapping sequences from two datatables?

## Issue

I have two data.tables that provide sequence coordinates across different chromosomes (categories). For example:

``````library(data.table)
dt1 <- data.table(chromosome = c("1", "1", "1", "1", "X"),
start = c(1, 50, 110, 150, 110),
end = c(11, 100, 121, 200, 200))
dt2 <- data.table(chromosome = c("1", "1", "X"),
start = c(12, 60, 50),
end = c(20, 115, 80))
``````

I need to create a third data.table that provides coordinates for sequences that contain all the integers in dt1 that do not overlap with any integers from the sequences in dt2. For example:

``````dt3 <- data.table(chromosome = c("1", "1", "1", "1", "X"),
start = c(1, 50, 116, 150, 110),
end = c(11, 59, 121, 200, 200))
``````

The data.tables I need to run this on are very large and therefore I need to maximise performance. I have tried using the foverlaps() function but to no avail. Any help would be greatly appreciated!

## Solution

You can start with something like this from `foverlaps`

``````setkey(dt2,chromosome,start,end)
ds = foverlaps(dt1,dt2,  type="any")
ds[,.(chromosome,
start = fcase(is.na(start) | i.start <= start,i.start,
i.end >= end, end + 1),
end = fcase(is.na(end) | i.end >= end, i.end,
i.start <= start, start - 1)
)]
#   chromosome start   end
#       <char> <num> <num>
#1:          1     1    11
#2:          1    50    59
#3:          1   116   121
#4:          1   150   200
#5:          X   110   200
``````