I want to permutation tests of the full GWAS using "GWASTools". In each permutation, responses are randomly permuted and I am interested in obtaining the p-value for each test of total genomic effect. Since the MAF and other stats are fixed, evaluating them in the permutations is unnecessary. Can I speed up the "assocRegression" function so that it only evaluates the p-value for each test?

Thank you.

There is no way to turn off computing the MAF, but I don't think you would see much of a time difference regardless. The MAF calculation is very fast compared with running the regression for each SNP. I'm not sure which "other stats" you're referring to, but they either take a negligible amount of time (EAF, n) or will change with each permutation (Est, SE, etc.)