Table 7 Power (when effect size is 0.3 or 0.6) in the simulation studies
From: SNP-PRAGE: SNP-based parametric robust analysis of gene set enrichment
Effect size (=β) | Causal gene set | Gene set size | Gene size | significance level | Z-statistic method | SNP-PRAGE | GLOSSI | GSEA | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Â | Â | Â | Â | Â | m | m | Â | Â | ||||||||
| Â | Â | Â | Â | Â | 1 | 2 | 3 | 4 | 5 | 1 | 2 | 3 | 4 | 5 | Â | Â |
0.3 | Set1 | 20 genes | 9~12 SNPs | 0.05 0.01 | .81 .78 | .81 .75 | .74 .66 | .67 .55 | .59 .38 | .92 .90 | .92 .91 | .94 .92 | .95 .92 | .95 .91 | .92 .89 | .95 .91 |
| Â | Set3 | 20 genes | 20 ~30 SNPs | 0.05 0.01 | .85 .76 | .78 .75 | .79 .74 | .79 .74 | .76 .73 | .81 .71 | .81 .73 | .83 .73 | .82 .74 | .83 .74 | .82 .72 | .83 .71 |
| Â | Set5 | 20 genes | 36~49 SNPs | 0.05 0.01 | .98 .95 | .99 .97 | .99 .97 | .99 .99 | .99 .98 | .74 .61 | .74 .62 | .75 .62 | .75 .62 | .76 .63 | .74 .60 | .73 .61 |
0.6 | Set1 | 20 genes | 9~12 SNPs | 0.05 0.01 | .84 .80 | .83 .75 | .78 .69 | .69 .60 | .62 .48 | .97 .94 | .98 .95 | .98 .97 | .98 .97 | .97 .96 | .98 .96 | .98 .97 |
| Â | Set3 | 20 genes | 20 ~30 SNPs | 0.05 0.01 | .86 .78 | .89 .82 | .86 .79 | .88 .80 | .88 .79 | .84 .75 | .85 .74 | .86 .75 | .86 .75 | .87 .76 | .84 .73 | .85 .74 |
| Â | Set5 | 20 genes | 36~49 SNPs | 0.05 0.01 | 1.0 .99 | .99 .97 | 1.0 .99 | 1.0 .99 | 1.0 .99 | .79 .69 | .80 .71 | .80 .72 | .82 .72 | .82 .73 | .79 .69 | .79 .68 |