Table 3. The evaluation performance of the pipeline for the simulated SNPs.

Random Forests (RF) Run				RF+Stepwise	RF+Ridge regression	RF+Lasso
#Iterations	Number of trees (ntree)	% Variance all (p) SNPs	% Variance k SNPs	Model significance (r-squared & p-values)	Model significance (%Variance)	Model significance (r-squared & p-values)
1	500	1.14	11.84	0.12 & 7.342e-12	24.36	0.14 & 2.482e-13
2	1000	1.71	16.36	0.14 & 1.042e-13	27.51	0.20 & 2.2e-16
3	2000	2.55	21.31	0.15 & 1.082e-14	28.97	0.22 & 2.2e-16
4	3000	1.6	19.34	0.13 & 1.604e-12	28.2	0.19 & 2.2e-16