LD group | # SNPs in LD group | LM | LME | FBAT | LM-LME 1 | Three-stage |
---|
0 <r2 ≤ 0.01 | 34025 | 0.20 | 0 | 0.01 | 0 | 0 |
0.01 <r2 ≤ 0.1 | 209 | 0.02 | 0.01 | 0 | 0.01 | 0 |
0.1 <r2 ≤ 0.3 | 6 | 0.70 | 0.54 | 0 | 0.54 | 0.50 |
0.3 <r2 ≤ 0.8 | 15 | 1 | 1 | 0.39 | 1 | 0.99 |
0.8 <r2 ≤ 1 | 10 | 1 | 1 | 0.51 | 1 | 0.99 |
- rs1570092 explains 1% phenotype variation.
- Marginal phenotype distribution follows a normal distribution with variance 1. The additive genetic effect is sqrt(0.01/2/0.31/0.69) = 0.153.
- LM_LME1: two-stage approach with LM at first stage with p-value cut-off 0.1, and LME at second stage with p-value cut-off 1e-6.
- Three-stage: LM at first stage with p-value cut-off 0.1, LME at second stage with p-value cut-off 1e-6 and FBAT at third stage with p-value cut-off 0.05/n, where n is the number of SNPs entering the third stage.