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. 2020 Oct 23;16(10):e1009141. doi: 10.1371/journal.pgen.1009141

Table 1. R2 values for height (without refitting).

For sequential LR, lasso and relaxed lasso, the chosen model is based on maximum R2 on the validation set. Model (3) to (9) each includes Model (2) plus their own specification as stated in the Form column. The elastic-net picks α = 0.9 based on the validation performance.

Model Form Rtrain2 Rval2 Rtest2 Size
(1) Age + Sex 0.5300 0.5260 0.5288 2
(2) Age + Sex + 10 PCs 0.5344 0.5304 0.5336 12
(3) Strong Single SNP 0.5364 0.5323 0.5355 13
(4) 10K Combined 0.5482 0.5408 0.5444 10,012
(5) 100K Combined 0.5833 0.5515 0.5551 100,012
(6) Sequential LR 0.7416 0.6596 0.6601 17,012
(7) Lasso 0.8304 0.6992 0.6999 47,673
(8) Relaxed Lasso 0.7789 0.6718 0.6727 13,395
(9) Elastic Net 0.8282 0.6991 0.6998 48,268