. 2021 Jun 3;45(6):577–592. doi: 10.1002/gepi.22393

Table 1.

Data‐generating models in the absence of SNP × Sex interaction effects using (a) XCI (Clayton) coding and (b) eXCI (PLINK) coding

Coding				Model coefficients		OR for effect of sex	ORs for effect of SNP, given sex			Prevalence
Sex	# Copies of effect allele			β_sex	β_SNP	OR_sex (e^β ^sex)	OR_SNP\|M (e^2βSNP)	OR_SNP\|W1 (e^βSNP)	OR_SNP\|W2 (e^2βSNP)	Overall	Female	Male
	(a) XCI (Clayton) coding
	0	1	2	0	0.75	e⁰	e^1.5	e^0.75	e^1.5	0.664	0.668	0.660
M	0	2	NA	0.1	0.5	e^0.1	e¹	e^0.5	e¹	0.628	0.618	0.638
F	0	1	2	0.2	0.2	e^0.2	e^0.4	e^0.2	e^0.4	0.574	0.550	0.598
				0.5	0.1	e^0.5	e^0.2	e^0.1	e^0.2	0.585	0.514	0.646
				0.75	0	e^0.75	e⁰	e⁰	e⁰	0.589	0.500	0.678
	(b) eXCI (PLINK) coding
	0	1	2	0	0.75	e⁰	e^0.75	e^0.75	e^1.5	0.629	0.668	0.590
M	0	1	NA	0.1	0.5	e^0.1	e^0.5	e^0.5	e¹	0.602	0.618	0.586
F	0	1	2	0.2	0.2	e^0.2	e^0.2	e^0.2	e^0.4	0.562	0.550	0.574
				0.5	0.1	e^0.5	e^0.1	e^0.1	e^0.2	0.579	0.524	0.634
				0.75	0	e^0.75	e⁰	e⁰	e⁰	0.589	0.500	0.678

Note: With the coding scheme used when generating the data specified on the left, we give how SNPs are coded within sex under each coding scheme. The “Model” column provides the five coefficient combinations we used to generate the data in this simulation study. We then calculated the odds ratio for the effect of sex and for the effect of SNP given sex. OR_sex refers to the odds ratio for the effect of sex with female as the reference level and male equal to 1. OR_SNP|M refers to the odds ratio for the effect of SNP, either comparing SNP = 0 with SNP = 2 in XCI (Clayton) or with SNP = 1 in eXCI (PLINK) coding, given sex = male. OR_SNP|W1 refers to the odds ratio for the effect of SNP comparing SNP = 0 with SNP = 1 and OR_SNP|W2 refers to the odds ratio for the effect of SNP comparing SNP = 0 with SNP = 2, given sex = female. In the “Prevalence” column, we calculated the proportion of cases in the overall population (1000 cases), in females (500 cases), and in males (500 cases).