Table 1. Rejection rates (type I errors for JLIM and conditional, power for coloc and HEIDI).
q = 13. 1000 iterations. α = 0.05. The correlation is -0.69 between SNP 1 and SNP 3, 0.68 between SNP 1 and SNP 4, 0.02 between SNP 1 and SNP 5, -0.35 between SNP 4 and SNP 5. Different subjects for two traits. For CMC, B = 104. For MA, B = 103, u = 10 and s = 1.
| Causal locations for trait 1 (size) | Causal locations for trait 2 (size) | JLIM | Conditional | coloc | HEIDI** | |||
|---|---|---|---|---|---|---|---|---|
| 1st SNP | CB (w/o adj.) | CMC* | MA | |||||
| 1 (0.3) | None | 0.047 | 0.054 | 0.005 (0.079) | 0.031 (0.021)[0.015] |
0.020 | 0.056 | 0.194 (0.006) |
| 1 (0.3) | 3 (0.3) | 0 | 0.054 | 0.007 (0.117) | 0.039 (0.025) [0.018] | 0.025 | 0.964 | 0.076 (0.059) |
| 1 (0.3) | 4 (0.3) | 0 | 0.054 | 0.007 (0.121) | 0.039 (0.029)[0.020] | 0.030 | 0.974 | 0.040 (0.038) |
| 1 (0.3) | 4 (-0.3) | 0 | 0.054 | 0.007 (0.121) | 0.051 (0.029) [0.025] | 0.031 | 0.970 | 0.042 (0.040) |
| 1 (0.2), 5 (-0.3) | 4 (0.3) | 0.393 | 0.049 | 0.009 (0.145) | 0.048 (0.028)[0.022] | 0.030 | 0.932 | 0.090 (0.085) |
* The tuning parameter θ was chosen as 0.05 (0.1) [0.2].
** When there was no causal location for trait 2, HEIDI sometimes output NA (after detecting the violation of its assumptions). We thus recorded two ratios A (B). A: #rejected/#non-NA results. (B): #rejected/#iterations.