In the following, we first evaluate the performance of our tool, demonstrating its speed gains and robust control of type I error. Then, using precision-recall analyses, comparing small to large GWAS results for lipid traits and Crohn’s disease, we demonstrate that our pathway scoring approach exhibits a gain in power compared to binary enrichment. Finally, we apply our method to dozens of large meta-analysis studies and evaluate power by counting the number of pathways passing the Bonferroni-corrected p-value threshold.
