. 2014 May 8;197(3):823–838. doi: 10.1534/genetics.114.164814

Table 3. The power comparison (at P-value threshold of 10⁻⁸) between our LHS method (with a single EM run) and three other haplotype methods—Beagle in Browning and Browning (2007), FZ in Feng and Zhu (2010), and Whait in Li et al. (2010a)—under different simulation conditions.

	Conditions		Power
Case/control	Sporadic rate^a	Causal haplotypes	LHS	Beagle	FZ	Whait
1000/1000	0.01	2	1.00	0.99	0.99	0.97
		4	0.95	0.93	0.92	0.95
		8	0.71	0.60	0.64	0.64
	0.02	2	0.98	0.95	0.95	0.93
		4	0.93	0.74	0.89	0.87
		8	0.53	0.33	0.32	0.41
2000/2000	0.01	2	1.00	0.99	1.00	1.00
		4	0.98	0.98	0.98	0.99
		8	0.83	0.71	0.81	0.73
	0.02	2	0.98	0.96	0.98	0.98
		4	0.97	0.92	0.97	0.95
		8	0.71	0.56	0.68	0.63

Note that Beagle, FZ, and Whait require phased haplotypes for association and we supplied them with the true haplotypes; our LHS method used diplotypes.

The penetrance is assumed to be fixed at 0.10, so that a higher sporadic rate results in a lower power.

Table 3. The power comparison (at P-value threshold of 10−8) between our LHS method (with a single EM run) and three other haplotype methods—Beagle in Browning and Browning (2007), FZ in Feng and Zhu (2010), and Whait in Li et al. (2010a)—under different simulation conditions.

Table 3. The power comparison (at P-value threshold of 10⁻⁸) between our LHS method (with a single EM run) and three other haplotype methods—Beagle in Browning and Browning (2007), FZ in Feng and Zhu (2010), and Whait in Li et al. (2010a)—under different simulation conditions.