PLINK 1.0 also has association analysis and quality control routines which perform Fisher’s exact test on 2×2 and 2×3 tables, using the FEXACT network algorithm from Mehta et al. [15,16]. The 2×2 case has the same mathematical structure as the Hardy-Weinberg equilibrium exact test, so it was straightforward to modify the early-termination SNP-HWE algorithm to handle it. The 2×3 case is more complicated, but retains the property that only \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document} $O(\sqrt {\mathrm {\# of tables}})$ \end{document}O(#oftables) relative likelihoods need to be evaluated, so we were able to develop a function to handle it in O(n) time; see Figure 2 for more details. Our timing data indicate that our new functions are consistently faster than both FEXACT and the update to the network algorithm by Requena et al. [17].
