Journal of Probability and Statistics / 2012 / Article / Tab 6 / Research Article
A Two-Stage Penalized Logistic Regression Approach to Case-Control Genome-Wide Association Studies Table 6 Comparison of TPLR approach and LASSO-patternsearch (the PDR and FDR with subscript M , I , and S indicate the rates calculated for main-effect features, interaction features, and SNPs resp.)
TPLR Approach
𝛾
P
D
R
𝑀
F
D
R
𝑀
P
D
R
𝐼
F
D
R
𝐼
P
D
R
𝑆
F
D
R
𝑆
0.0 0.964 0.902 0.884 0.907 0.947 0.855 0.2 0.768 0.926 0.884 0.900 0.947 0.852 0.4 0.714 0.505 0.748 0.677 0.803 0.494 0.6 0.692 0.199 0.680 0.413 0.730 0.200 0.8 0.684 0.112 0.642 0.331 0.691 0.126 1.0 0.672 0.023 0.610 0.267 0.654 0.073 1.2 0.668 0.021 0.594 0.237 0.638 0.057 1.4 0.658 0.009 0.566 0.201 0.608 0.041 1.6 0.654 0.006 0.536 0.165 0.578 0.026 1.8 0.646 0.006 0.524 0.144 0.563 0.021 2.0 0.630 0.006 0.492 0.109 0.526 0.015 LASSO-patternsearch
𝛼
P
D
R
𝑀
F
D
R
𝑀
P
D
R
𝐼
F
D
R
𝐼
P
D
R
𝑆
F
D
R
𝑆
1
0
−
0
0.882 0.445 0.710 0.967 0.847 0.940
1
0
−
1
0.816 0.332 0.696 0.957 0.827 0.926
1
0
−
2
0.786 0.283 0.664 0.929 0.774 0.885
1
0
−
3
0.718 0.241 0.618 0.869 0.694 0.802
1
0
−
4
0.646 0.220 0.556 0.752 0.609 0.654
1
0
−
5
0.578 0.193 0.486 0.563 0.531 0.444
1
0
−
6
0.504 0.184 0.414 0.355 0.453 0.254
1
0
−
7
0.400 0.190 0.360 0.196 0.383 0.130
1
0
−
8
0.332 0.202 0.292 0.076 0.316 0.047