BMC Genomic Data

Table 4 Realized β^a, 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	Realized^a	Mean bias	Mean SE	Coverage	P < 0.05^b
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	Realized^a	Mean bias	Mean SE	Coverage	P < 0.05^b
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	Realized^a	Mean bias	Mean SE	Coverage	P < 0.05^b
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

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.

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