Table 1 Performances of Mondrian cross-conformal prediction at an error of 0.05 on various genetic architecture by simulation (proportion of discovery set for GWAS is 0.5).
Heritability | Polygenicity | Prevalence | AUC (95% CI) | PPV (95% CI) | NPV (95% CI) | Coverage |
---|---|---|---|---|---|---|
0.3 | 0.001 | 0.01 | 0.84 (0.80–0.88) | 0.48 (0.44–0.53) | 0.96 (0.94–0.98) | 0.18 |
0.05 | 0.81 (0.79–0.84) | 0.76 (0.73–0.80) | 0.81 (0.77–0.84) | 0.22 | ||
0.2 | 0.76 (0.73–0.79) | 0.75 (0.72–0.81) | 0.67 (0.61–0.72) | 0.17 | ||
0.01 | 0.01 | 0.78 (0.71–0.84) | 0.25 (0.19–0.35) | 0.97 (0.95–0.99) | 0.16 | |
0.05 | 0.75 (0.71–0.79) | 0.61 (0.57–0.65) | 0.82 (0.79–0.85) | 0.18 | ||
0.2 | 0.73 (0.70–0.77) | 0.69 (0.66–0.73) | 0.74 (0.71–0.78) | 0.17 | ||
0.1 | 0.01 | 0.67 (0.58–0.76) | 0.18 (0.13–0.33) | 0.95 (0.92–0.99) | 0.12 | |
0.05 | 0.67 (0.62–0.71) | 0.57 (0.52–0.63) | 0.74 (0.70–0.78) | 0.14 | ||
0.2 | 0.59 (0.55–0.64) | 0.65 (0.59–0.73) | 0.56 (0.53–0.61) | 0.12 | ||
0.2 | 0.01 | 0.68 (0.60–0.76) | 0.24 (0.20–0.29) | 0.94 (0.91–0.97) | 0.11 | |
0.05 | 0.70 (0.65–0.74) | 0.61 (0.57–0.65) | 0.76 (0.72–0.80) | 0.15 | ||
0.2 | 0.62 (0.58–0.67) | 0.65 (0.60–0.69) | 0.62 (0.58–0.66) | 0.16 | ||
0.5 | 0.001 | 0.01 | 0.91 (0.89–0.94) | 0.57 (0.52–0.61) | 0.98 (0.97–0.99) | 0.32 |
0.05 | 0.88 (0.86–0.90) | 0.81 (0.79–0.84) | 0.88 (0.86–0.90) | 0.30 | ||
0.2 | 0.83 (0.80–0.85) | 0.82 (0.79–0.84) | 0.78 (0.75–0.81) | 0.24 | ||
0.01 | 0.01 | 0.85 (0.81–0.90) | 0.39 (0.34–0.44) | 0.98 (0.96–0.99) | 0.23 | |
0.05 | 0.84 (0.82–0.87) | 0.72 (0.69–0.76) | 0.88 (0.86–0.90) | 0.26 | ||
0.2 | 0.80 (0.77–0.82) | 0.77 (0.74–0.80) | 0.79 (0.76–0.82) | 0.21 | ||
0.1 | 0.01 | 0.75 (0.69–0.81) | 0.28 (0.24–0.33) | 0.96 (0.94–0.98) | 0.15 | |
0.05 | 0.80 (0.77–0.83) | 0.69 (0.66–0.73) | 0.83 (0.81–0.86) | 0.21 | ||
0.2 | 0.70 (0.66–0.73) | 0.68 (0.64–0.72) | 0.71 (0.67–0.74) | 0.15 | ||
0.2 | 0.01 | 0.79 (0.73–0.85) | 0.20 (0.16–0.25) | 0.98 (0.96–1.00) | 0.17 | |
0.05 | 0.75 (0.72–0.79) | 0.64 (0.60–0.69) | 0.83 (0.80–0.86) | 0.19 | ||
0.2 | 0.68 (0.64–0.72) | 0.65 (0.61–0.70) | 0.68 (0.64–0.72) | 0.14 | ||
0.8 | 0.001 | 0.01 | 0.93 (0.90–0.95) | 0.50 (0.43–0.55) | 0.99 (0.98–1.00) | 0.42 |
0.05 | 0.92 (0.90–0.93) | 0.82 (0.79–0.85) | 0.94 (0.93–0.95) | 0.46 | ||
0.2 | 0.91 (0.90–0.92) | 0.88 (0.87–0.90) | 0.87 (0.85–0.89) | 0.39 | ||
0.01 | 0.01 | 0.91 (0.88–0.93) | 0.50 (0.46–0.55) | 0.98 (0.97–0.99) | 0.31 | |
0.05 | 0.91 (0.90–0.93) | 0.83 (0.80–0.85) | 0.93 (0.91–0.94) | 0.41 | ||
0.2 | 0.89 (0.87–0.90) | 0.85 (0.82–0.87) | 0.86 (0.84–0.88) | 0.33 | ||
0.1 | 0.01 | 0.84 (0.79–0.89) | 0.36 (0.31–0.42) | 0.98 (0.96–0.99) | 0.21 | |
0.05 | 0.86 (0.83–0.88) | 0.75 (0.72–0.78) | 0.89 (0.86–0.91) | 0.28 | ||
0.2 | 0.82 (0.79–0.84) | 0.78 (0.75–0.81) | 0.80 (0.77–0.83) | 0.22 | ||
0.2 | 0.01 | 0.75 (0.69–0.81) | 0.35 (0.30–0.40) | 0.94 (0.91–0.97) | 0.14 | |
0.05 | 0.84 (0.82–0.87) | 0.72 (0.69–0.76) | 0.88 (0.86–0.90) | 0.26 | ||
0.2 | 0.78 (0.75–0.81) | 0.73 (0.70–0.77) | 0.78 (0.75–0.81) | 0.20 |