. 2020 Apr 8;27(4):599–612. doi: 10.1089/cmb.2019.0325

Table 3.

Simulations with Infinitesimal Genetic Model and Population Structure

Model	mean( $β_{g 0}$ )	se( $β_{g 0}$ )	mean( $χ_{N u l l}^{2}$ )	se( $χ_{N u l l}^{2}$ )	mean( $β_{g}$ )	se( $β_{g}$ )	mean( $χ^{2}$ )	se( $χ^{2}$ )
LR	−1.2E-03	2.30E-03	2.94	0.14	0.250	2.20E-03	47.28	0.92
LR + 1 PC	−8.00E-04	2.10E-03	2.44	0.12	0.250	1.90E-03	48.20	0.85
LR + 2 PCs	−1.00E-04	1.80E-03	1.94	0.09	0.253	1.70E-03	49.00	0.80
LR + 3 PCs	−3.00E-04	1.60E-03	1.49	0.07	0.252	1.50E-03	48.90	0.76
LR + 4 PCs	1.00E-03	1.30E-03	1.02	0.05	0.250	1.30E-03	47.86	0.70
LR + cvBLUP	4.00E-04	1.20E-03	1.00	0.04	0.240	1.20E-03	56.8	0.81
LMM	−2.00E-04	1.20E-03	0.99	0.05	0.252	1.20E-03	56.97	0.79
BOLT-INF	−1.00E-04	1.00E-03	0.97	0.04	0.214	1.00E-03	54.34	0.76
BOLT-LMM	−1.00E-04	1.00E-03	0.97	0.04	0.214	1.00E-03	54.37	0.76
LR + true genetic effect	2.20E-03	1.80E-03	3.55	0.16	0.250	1.80E-03	89.28	1.56

Mean and standard error for effect estimates and test statistics of association tests at 1000 null SNPs with true $β = g 0 : \hat{β_{g 0}}$ and $χ_{N u l l}^{2}$ ; and at 1000 causal SNPs with an alternative hypothesis of true $β_{g} = 0.25 : {\hat{β}}_{g}$ and $χ^{2}$ .