I am running one burden test per enhancer region in about 14,000 enhancers.
So, I could correct by taking a threshold of 0.05 / 14000.
However, some of these enhancers are actually exactly the same, but being tested twice due to being active in more than one cell type. Others are distinct enhancers, but the sequence is anywhere from 5-95% overlapping another enhancer.
My question is, how should I go about establishing a bonferonni-corrected threshhold for association?
Clearly this are not independent tests, which is normally when a BCT is invoked. So what is the best fix here?
I want to run all the tests because I want to know if the same, or similar, enhancers are acting in different cells, so I do not wish the redundancy before running the tests. Rather, I seek a way of altering the threshhold in such a way that recognizes that in some case it is the same test being run, it is just that the enhancer is active in 2 (or more) cell types.