Perform fisher’s exact test on the number of overlaps/unique intervals between 2 files. Traditionally, in order to test whether 2 sets of intervals are related spatially, we resort to shuffling the genome and checking the simulated (shuffled) versus the observed. We can do the same analytically for many scenarios using Fisher’s Exact Test. This implementation can calculate the number of overlaps and the number of intervals unique to each file and it infers (or accepts) the number that are not present in each file.
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