Haplin power analysis: a software module for power and sample size calculations in genetic association analyses of family triads and unrelated controls

Table 3 Examples of asymptotic power calculations in Haplin

Effects	Haplin commands	Output
a) Child	hapPowerAsymp(cases = c(mfc=500),	$haplo.power
	haplo.freq = c(0.8,0.2),	Haplotype RR.power
	RR = c(1,1.4))	1 ref
		2 0.88
b) PoO	hapPowerAsymp(cases = c(mfc=500),	$haplo.power
	haplo.freq = c(0.8,0.2),	Haplotype RRcm.power RRcf.power RRcm_cf.power
	RRcm = c(1,2), RRcf = c(1,1.5))	1 ref ref ref
		2 1 0.87 0.48
c) Child and maternal	hapPowerAsymp(cases = c(mfc=500),	$haplo.power
	haplo.freq = c(0.8,0.2),	Haplotype RR.power RRm.power
	RR = c(1,1.4), RR.mat = c(1,1.2))	1 ref ref
		2 0.9 0.42
d) PoO and maternal	hapPowerAsymp(cases = c(mfc=500),	$haplo.power
	haplo.freq = c(0.8,0.2),	Haplotype RRcm.power RRcf.power RRcm_cf.power RRm.power
	RRcm = c(1,2), RRcf = c(1,1.5),	1 ref ref ref ref
	RR.mat = c(1,1.2))	2 0.99 0.65 0.2 0.17

The power is calculated for a diallelic SNP, using 500 case-parent triads (cases = c(mfc=500)), and a MAF of 0.2 (haplo.freq = c(0.8,0.2)). The argument RR specifies the relative risk associated with the child effect, whereas the power to detect a PoO effect is calculated by replacing RR by the two relative risk arguments RRcm and RRcf, which refer to the parental origin of the allele carried by the child. Maternal effects can be included by adding the maternal relative risk parameter RR.mat to the original child or PoO command. Note that the order of alleles to which the relative risk parameters refer corresponds to the order used for the haplotype frequencies. Here, the less frequent allele is set as the risk allele and the more frequent allele is used as reference. The nominal significance level defaults to 0.05, but other values can be specified by the argument alpha

ISSN: 1471-2105