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.

Thank you for the prompt reply!