I would like to run a fishers exact test using bedtools fisher. I have two files to test the overlap, and a genome file. However, the result does not give me an odds ratio, and the number of possible intervals is the same number as the number of query intervals. I have ran the same code with different files and it works fine, so I am not sure what is going on here. See the result below:
# Number of query intervals: 962714 # Number of db intervals: 18661 # Number of overlaps: 516254 # Number of possible intervals (estimated): 962714 # phyper(516254 - 1, 962714, 962714 - 962714, 18661, lower.tail=F) # Contingency Table Of Counts #_________________________________________ # | in -b | not in -b | # in -a | 516254 | 446460 | # not in -a | 0 | 0 | #_________________________________________ # p-values for fisher's exact test left right two-tail ratio 1 1 1 -nan
How would one interpret this result and could there be an issue with the files?