Figure 1.
Quantile-quantile plot of significance level and Type I error rate.
The Type I error is evaluated by GEE-GMDR method with digenic, trigenic and tetragenic models in presence of no gene-gene interaction and no residual correlation. The reference line is a diagonal line with unit slope through the origin. An unbiased method is expected to give the points falling on or near the reference line (i.e., Type I error rate is very close to the nominal level).
Table 1.
Type I error rates for GEE-GMDR and GMDR methods.
Figure 2.
Comparison of statistical power between univarate GMDR method and GEE-GMDR under digenic, trigenic and tetragenic interaction models.
The horizontal axis represents different residual correlations. The empirical statistical power is defined as the proportion of significant true models at 5% level in 200 simulations.
Table 2.
Comparison of Cross-Validation Consistency (CVC) and Test Accuracy (TA) between GEE-GMDR and the GMDR method for two simulated continuous traits.
Figure 3.
The principal components analysis for SAGE.
The first two principal components are plotted to represent genetic background of the SAGE.
Figure 4.
The interaction pattern among rs2072660-rs1209068-rs11030134-rs6011770.
The left bar in each nonempty cell denotes a positive score and the right bar a negative score. High-risk cells are indicated by dark shading, low-risk cells by light shading, and empty cells by no shading. Note that the patterns of high-risk and low-risk cells differ across each of the different multilocus dimensions, presenting evidence of epistasis.
Table 3.
Interaction SNPs detected among CHRNB2, NTRK2, BDNF, and CHRNA4.
Table 4.
Information on the SNPs in the best model identified using GEE-GMDR method.