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I used findOverlap() function that takes two bed file as argument to check overlapped genomic interval. this function truly returned bunch of overlapped interval. Now I want to know what's combined p-value of these overlapped interval by using Fisher' exact test. What's the simplest approach for this case? Thanks all

To calculate the combined p-value of overlapped genomic intervals, you can use Fisher's exact test. Merge the overlapping intervals into non-overlapping regions. You can use a tool like bedtools merge or bedops to do this. The resulting regions will represent the non-redundant genomic intervals that are covered by the original intervals. How to do simple Fisher' exact test for overlapped genomic interval in R? bitlife