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Table 4 Realized βa, mean bias, mean standard error (SE), coverage probability and percentage of the effects that had a p-value < 0.05 in the simulation where haplotypes 001 and 101 had a modeled parameter estimate of 1.10. Each replicate contained 2000 individuals.

From: Estimating effects of rare haplotypes on failure time using a penalized Cox proportional hazards regression model

No penalty
Haplotype Frequency Realizeda Mean bias Mean SE Coverage P < 0.05b
001 0.050 1.094 -0.005 0.08 0.93 1.00
101 0.003 1.155 -0.037 0.38 0.93 0.77
010 0.020 0.016 -0.007 0.14 0.98 0.02
011 0.005 0.023 0.036 0.30 0.98 0.02
100 0.020 0.006 0.015 0.14 1.00 0.00
110 0.002 0.084 0.075 1.14 0.95 0.05
111 0.280 -0.007 -0.007 0.03 0.82 0.18
Ridge penalty
Haplotype Frequency Realizeda Mean bias Mean SE Coverage P < 0.05b
001 0.050 1.094 -0.009 0.07 0.91 1.00
101 0.003 1.155 -0.085 0.61 0.91 0.62
010 0.020 0.016 -0.007 0.013 0.96 0.04
011 0.005 0.023 0.046 0.23 0.96 0.04
100 0.020 0.006 0.014 0.12 0.98 0.02
110 0.002 0.084 0.067 0.40 0.66 0.34
111 0.280 -0.007 -0.008 0.03 0.81 0.19
Difference penalty
Haplotype Frequency Realizeda Mean bias Mean SE Coverage P < 0.05b
0 0 1 0.050 1.094 -0.011 0.07 0.88 1.00
1 0 1 0.003 1.155 -0.066 0.54 0.88 0.71
0 1 0 0.020 0.016 0.004 0.12 0.96 0.04
0 1 1 0.005 0.023 0.071 0.22 0.90 0.10
1 0 0 0.020 0.006 0.017 0.12 0.98 0.02
1 1 0 0.002 0.084 0.069 0.37 0.57 0.43
1 1 1 0.280 -0.007 -0.009 0.03 0.82 0.18
  1. a) "Realized" denotes to the median estimate from the simulated data, where the haplotypes were known, and could be used in the Cox model directly; b) For haplotypes 001 and 101 these percentages reflect power, whereas the percentages for the other five haplotypes reflect type I error probabilities.