p-values of fisher exact test (and likelihood)

fisherOR.jl

using Distributions
using Plots


function Fishertest(X, phi)
    cs = sum(X, dims=1)
    rs = sum(X, dims=2)
    f(x, phi) = pdf(FisherNoncentralHypergeometric(cs[1],cs[2],rs[1], exp(phi)), x)
    prob = f.(0:cs[1], phi)
    return sum(prob[prob .<= prob[X[1,1]+1]])
end 

X = [12 6; 5 12]

pfun(phi) = Fishertest(X, phi)
plot(x->pfun(x), label="p-value")
cs = sum(X, dims=1)
rs = sum(X, dims=2)
f(phi) = pdf(FisherNoncentralHypergeometric(cs[1],cs[2],rs[1], exp(phi)),X[1,1])
plot!(x->f(x), label="likelihood")