I am trying to reproduce a functional enrichment analysis with Mummichog from the web app with the R package. For this I have to set a p-value cutoff with the `SetMummichogPval()` function. As standard settings, the web app claims to use the top 10 % peaks. To reproduce this in R, I ranked the features according to their p-values in an ascending order (lowest p-values/highest significance at the top) and I took the lowest value from the most significant 10 % (= the 10th percentile) as the cutoff. When I did it like this, the value I got was around 0.008. The web app, which claims to do the same thing, gives me a cutoff of 0.005 and with this value I get slightly different results from the enrichment analysis. I concluded that the value is somehow rounded in the web app in a way that is not documented (at least I couldn’t find it). I played around with different input files but could not figure out exactly how the rounding is done.
Could you please explain how the rounding is done in the web app?