Fig. 1

Comparing logistic regression and Cox regression on data simulated from either a logistic model or a Cox model (1000 simulations each). Each simulation included 100 risk alleles and 799,900 alleles not associated with the phenotype. True positive rate was calculated as the fraction of risk alleles having Bonferroni-adjusted p-value less than the given cutoff. a Boxplots of true positive rate for logistic regression, Cox regression, and the sequential strategy, across simulations from each simulation model. The sequential strategy used the p-value from Cox regression, if the unadjusted p-value from logistic regression was ≤10^− 4. For ease of visualization, outliers are not shown. b 95% confidence intervals of the difference between the true positive rates of Cox and logistic regression