Table 6.
List of SNPs selected by the SMCP and the LASSO method for a simulated data set with binary trait. The analysis is based on marginal least-square loss. Recall that the 31 disease-associated SNPs are 2287–2298 and 2300–2318
| SNP | SMCP
|
MCP
|
LASSO
|
Regression
|
||||
|---|---|---|---|---|---|---|---|---|
| |β̂| | p-value* | |β̂| | p-value* | |β̂| | p-value* | |β̂| | p-value** | |
| 366 | −0.002 | 1.000 | −0.002 | 1.000 | −0.071 | 0.004 | ||
| 368 | −0.002 | 1.000 | −0.012 | 1.000 | −0.010 | 1.000 | −0.075 | 0.002 |
| 506 | −0.005 | 1.000 | −0.025 | 1.000 | −0.021 | 1.000 | −0.081 | 0.001 |
| 656 | 0.002 | 1.000 | 0.015 | 1.000 | 0.012 | 1.000 | 0.077 | 0.002 |
| 932 | 3.4E-04 | 1.000 | 2.9E-04 | 1.000 | 0.071 | 0.005 | ||
| 948 | 0.001 | 1.000 | 0.005 | 1.000 | 0.004 | 1.000 | 0.073 | 0.004 |
| 1047 | 0.002 | 1.000 | 0.002 | 1.000 | 0.071 | 0.004 | ||
| 1476 | 0.000 | 1.000 | −0.001 | 1.000 | −0.001 | 1.000 | −0.071 | 0.005 |
| 1477 | 0.001 | 1.000 | 0.006 | 1.000 | 0.005 | 1.000 | 0.073 | 0.003 |
| 1478 | −0.001 | 1.000 | −0.003 | 1.000 | −0.002 | 1.000 | −0.072 | 0.004 |
| 1678 | −0.002 | 1.000 | −0.009 | 1.000 | −0.007 | 1.000 | −0.074 | 0.003 |
| 1978 | −0.013 | 0.240 | −0.049 | 0.230 | −0.041 | 0.230 | −0.091 | 2.6E-04 |
| 1980 | −0.001 | 1.000 | −0.007 | 1.000 | −0.006 | 1.000 | −0.073 | 0.003 |
| 1990 | 0.008 | 1.000 | 0.018 | 1.000 | 0.015 | 1.000 | 0.078 | 0.002 |
| 2048 | 0.003 | 1.000 | 0.009 | 1.000 | 0.008 | 1.000 | 0.074 | 0.003 |
| 2284 | −0.009 | 1.000 | −0.028 | 1.000 | −0.023 | 1.000 | −0.082 | 0.001 |
| 2285 | 0.005 | 1.000 | 0.060 | 0.016 | ||||
| 2286 | −0.076 | 0.006 | −0.102 | 0.006 | −0.085 | 0.006 | −0.113 | 4.9E-06 |
| 2287 | 0.049 | 0.250 | 0.043 | 0.442 | 0.036 | 0.442 | 0.088 | 3.9E-04 |
| 2288 | 0.051 | 0.222 | 0.047 | 0.282 | 0.039 | 0.282 | 0.090 | 2.9E-04 |
| 2289 | −0.060 | 0.206 | −0.044 | 0.328 | −0.037 | 0.328 | −0.089 | 3.6E-04 |
| 2290 | 0.093 | 0.001 | 0.177 | 0.001 | 0.147 | 0.001 | 0.144 | 4.2E-09 |
| 2291 | −0.003 | 1.000 | −0.054 | 0.031 | ||||
| 2293 | 0.051 | 0.028 | 0.109 | 0.028 | 0.091 | 0.028 | 0.116 | 2.8E-06 |
| 2294 | 0.049 | 0.153 | 0.069 | 0.259 | 0.058 | 0.259 | 0.099 | 6.2E-05 |
| 2295 | −0.028 | 0.187 | −0.042 | 0.500 | −0.035 | 0.500 | −0.088 | 3.9E-04 |
| 2296 | 0.007 | 1.000 | 0.061 | 0.014 | ||||
| 2300 | 0.122 | 0.009 | 0.138 | 0.009 | 0.115 | 0.009 | 0.128 | 2.1E-07 |
| 2301 | −0.148 | 4.2E-05 | −0.240 | 4.2E-05 | −0.200 | 4.2E-05 | −0.170 | 2.4E-12 |
| 2302 | 0.126 | 0.003 | 0.158 | 0.003 | 0.131 | 0.003 | 0.136 | 3.0E-08 |
| 2303 | −0.040 | 0.707 | −0.048 | 0.053 | ||||
| 2304 | −0.090 | 0.001 | −0.207 | 0.001 | −0.172 | 0.001 | −0.157 | 1.4E-10 |
| 2305 | −0.060 | 0.027 | −0.113 | 0.027 | −0.095 | 0.027 | −0.118 | 1.9E-06 |
| 2306 | 0.007 | 1.000 | 0.020 | 0.421 | ||||
| 2307 | −0.001 | 1.000 | −0.001 | 1.000 | −0.001 | 1.000 | −0.071 | 0.005 |
| 2309 | 0.030 | 0.081 | 0.076 | 0.081 | 0.064 | 0.081 | 0.102 | 3.7E-05 |
| 2310 | −0.024 | 0.313 | −0.035 | 0.689 | −0.029 | 0.689 | −0.085 | 0.001 |
| 2316 | −0.010 | 0.299 | −0.050 | 0.214 | −0.041 | 0.214 | −0.091 | 2.4E-04 |
| 2329 | 0.001 | 1.000 | 0.001 | 1.000 | 0.071 | 0.005 | ||
| 2337 | −0.022 | 0.238 | −0.063 | 0.238 | −0.052 | 0.238 | −0.097 | 9.8E-05 |
| 2360 | −0.005 | 1.000 | −0.014 | 1.000 | −0.012 | 1.000 | −0.076 | 0.002 |
| 2362 | −0.002 | 1.000 | −0.007 | 1.000 | −0.006 | 1.000 | −0.073 | 0.003 |
| 2461 | 0.002 | 1.000 | 0.011 | 1.000 | 0.010 | 1.000 | 0.075 | 0.003 |
| 2550 | 0.003 | 1.000 | 0.068 | 0.007 | ||||
| 2551 | 0.031 | 0.172 | 0.055 | 0.172 | 0.046 | 0.172 | 0.093 | 1.7E-04 |
| 2552 | −0.022 | 0.639 | −0.034 | 1.000 | −0.028 | 1.000 | −0.085 | 0.001 |
| 2553 | 0.018 | 0.768 | 0.037 | 0.902 | 0.031 | 0.902 | 0.086 | 0.001 |
| 2912 | 0.003 | 1.000 | 0.008 | 1.000 | 0.007 | 1.000 | 0.074 | 0.003 |
| 3140 | 0.004 | 1.000 | 0.016 | 1.000 | 0.014 | 1.000 | 0.077 | 0.002 |
| 3329 | 0.016 | 1.000 | 0.029 | 1.000 | 0.024 | 1.000 | 0.083 | 0.001 |
| 3388 | 0.003 | 1.000 | 0.012 | 1.000 | 0.010 | 1.000 | 0.075 | 0.002 |
| 3620 | 0.002 | 1.000 | 0.013 | 1.000 | 0.011 | 1.000 | 0.076 | 0.002 |
| 4018 | 0.011 | 0.124 | 0.057 | 0.124 | 0.047 | 0.124 | 0.094 | 1.5E-04 |
| 4078 | 0.004 | 1.000 | 0.015 | 1.000 | 0.013 | 1.000 | 0.077 | 0.002 |
| 4745 | −0.002 | 1.000 | −0.001 | 1.000 | −0.071 | 0.004 | ||
| 4877 | 0.002 | 1.000 | 0.002 | 1.000 | 0.071 | 0.004 | ||
*
Computed using the multi-split method.
**
Single SNP analysis, not corrected for multiple testing.
***
Empty cells stand for SNPs that are not identified from the model.