## 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
```

Answered By – Peace Wang

Answer Checked By – David Marino (BugsFixing Volunteer)