Suppose I have done two Chip-seq experiments. Now after the bias correction step such as MACS2, I get two set of genomic intervals (or peaks, as what is usually called) that corresponds to each of the experiment. I want to test the significance of the overlap of these two set genomic intervals that corresponds to each experiment.
The common test employed seemed to me is the Hypergeometic test. There's even a package specifically aim for this task: ChiPpeakAnno.
Recall from the Hypergeometric distrbition -- the analogy is that we have a bag of marbles with two different colors, say one blue and another red. A sample from such distribution consists of marbles drawn from this bag, and a probability measure for this distribution is the number of blue marbles in the sample.
Could someone explain what is the correspondence between the hypergeometric test and the significance overlap between two different set of genomic intervals?