Table 1. Number of genes that pass R2 threshold.
R2 threshold | KNN | Elastic-Net | Combined | Single SNP | All models |
0.05 | 273/622 | 388/640 | 401/493 | 533/2659 | 700/2730 |
0.1 | 152/350 | 239/389 | 213/265 | 272/685 | 364/753 |
0.2 | 47/125 | 114/189 | 82/105 | 100/179 | 143/245 |
0.3 | 18/57 | 54/94 | 35/42 | 50/72 | 73/115 |
0.4 | 8/29 | 32/55 | 15/20 | 14/25 | 36/62 |
0.5 | 4/17 | 14/28 | 6/11 | 5/7 | 16/29 |
Models are: K-nearest-neighbor (KNN); Regularized Linear model (Elastic-Net); single best-SNP (Single SNP) or in any one of them (All models). Shown are the number of genes that pass training and test R2 threshold (test/training) using the different models in the Cross-Pop cross-validation scheme.