From: Robust methods for population stratification in genome wide association studies
Case control | Testing SNP | Trend | GC | PCA | MDS | RPCA- | RPCA- |
---|---|---|---|---|---|---|---|
Difference | Types | Â | Â | Â | Â | RHM | PP |
S1 | Random SNPs | 2.75 | 1.41 | 1.94 | 0.97 | 1.01 | 0.99 |
(2 populations, moderate) | Differentiated SNPs | 99.85 | 98.75 | 93.03 | 1.33 | 0.99 | 1.00 |
Causal SNPs | 48.97 | 37.55 | 48.33 | 46.95 | 44.69 | 45.06 | |
S2 | Random SNPs | 16.74 | 1.71 | 8.38 | 1.09 | 0.99 | 1.00 |
(2 populations, more extreme) | Differentiated SNPs | 100.00 | 100.00 | 100.00 | 6.91 | 1.14 | 1.29 |
Causal SNPs | 49.94 | 14.09 | 44.77 | 32.81 | 30.07 | 30.21 | |
S3 | Random SNPs | 3.40 | 1.12 | 1.65 | 1.08 | 1.06 | 1.06 |
(3 populations, moderate) | Differentiated SNPs | 100.00 | 99.99 | 63.28 | 1.36 | 1.02 | 1.02 |
Causal SNPs | 48.85 | 31.61 | 46.72 | 45.81 | 43.29 | 43.89 | |
S4 | Random SNPs | 21.35 | 1.15 | 9.82 | 1.10 | 0.92 | 0.97 |
(3 populations, more extreme) | Differentiated SNPs | 100.00 | 100.00 | 100.00 | 18.13 | 1.29 | 1.51 |
Causal SNPs | 50.09 | 9.41 | 37.56 | 21.76 | 18.66 | 18.81 |