I'm trying to use IHW package to achieve covariate weighted p-values for about 35 million hypothesis testings, but the function has been running for 5 hours and still hasn't returned or thrown an error. I'm wondering if 35 million is stretching its scale and what would be the maximal amount of hypothesis it could reasonably handle. Besides, are there any way to speed it up?
pval.nb.ihw.refd = ihw(rand.p ~ ref.d, data = pval.nb, alpha = 0.05)
nrow(pval.nb)  353793300