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Table 2 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 with a rare allele at locus 2 had a modeled parameter estimate of 0.69. Each replicate contained 200 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
010 0.020 0.741 0.014 0.44 0.95 0.43
011 0.005 0.593 -0.663 2971.81 0.95 0.21
110 0.002 0.000 -0.971 14514.13 0.96 0.10
111 0.280 0.713 0.018 0.09 0.79 1.00
001 0.050 0.012 0.050 0.28 0.91 0.09
100 0.020 0.038 0.010 33.23 0.95 0.05
101 0.003 0.000 -2.212 7674.81 0.90 0.10
Ridge penalty
Haplotype Frequency Realizeda Mean bias Mean SE Coverage P < 0.05b
010 0.020 0.741 -0.135 0.73 0.85 0.18
011 0.005 0.593 -0.359 1.91 0.74 0.03
110 0.002 0.000 -0.557 1.00 0.39 0.19
111 0.280 0.713 -0.010 0.11 0.83 1.00
001 0.050 0.012 0.037 0.24 0.87 0.13
100 0.020 0.038 0.070 1.08 1.00 0.00
101 0.003 0.000 -0.649 2.16 0.89 0.11
Difference penalty
Haplotype Frequency Realizeda Mean bias Mean SE Coverage P < 0.05b
010 0.020 0.741 -0.008 0.62 0.98 0.35
011 0.005 0.593 -0.132 1.39 1.00 0.03
110 0.002 0.000 -0.272 1.00 1.00 0.15
111 0.280 0.713 0.008 0.12 0.89 1.00
001 0.050 0.012 0.122 0.24 0.79 0.21
100 0.020 0.038 0.131 0.88 0.93 0.07
101 0.003 0.000 -0.301 1.68 0.91 0.09
  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 010, 011, 110 and 111 these percentages reflect power, whereas the percentages for the other three haplotypes reflect type I error probabilities.
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BMC Genomic Data

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