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
you can't simply apply fisher's exact test as the population is unknown.
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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
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I was unable to find the overlapping genome because it is too old to use ragdoll archers