provide quantitative estimates of these limitations, and indications of possible limiting factors. For example, we found that power levels increase considerably with gene set size, fraction of causal genes in a gene set, and effect size of associated SNPs, and decrease with total number of causal genes in the genome. Similar trends, as a function of effect size and fraction of causal SNPs, have been shown with other types of GSEA methods that test for enrichment in SNP sets across pathways [32], [33].
