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

Table 2.

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

				Model			ORs for effect of sex, given SNP		ORs for effect of SNP, given Sex			Prevalence
Sex	# Copies of effect allele			β_sex	β_SNP	β_int	OR_sex\|SNP0 (e^βsex)	OR_sex\|SNP2 (e^βsex+2βint)	OR_SNP\|M (e^{2βSNP+2βint})	OR_SNP\|W1 (e^βSNP)	OR_SNP\|W2 (e^2βSNP)	Overall	Female	Male
	(a) XCI (Clayton) coding
	0	1	2	0.2	0.2	0.1	e^0.2	e^0.4	e^0.6	e^0.2	e^0.4	0.585	0.550	0.620
M	0	2	NA	0.2	0.2	0.2	e^0.2	e^0.6	e^0.8	e^0.2	e^0.4	0.595	0.550	0.640
F	0	1	2	0.2	0.2	0.3	e^0.2	e^0.8	e¹	e^0.2	e^0.4	0.604	0.550	0.658
	(b) eXCI (PLINK) coding
	0	1	2	0.2	0.2	0.1	e^0.2	e^0.3	e^0.3	e^0.2	e^0.4	0.568	0.550	0.586
M	0	1	NA	0.2	0.2	0.2	e^0.2	e^0.4	e^0.4	e^0.2	e^0.4	0.574	0.550	0.598
F	0	1	2	0.2	0.2	0.3	e^0.2	e^0.5	e^0.5	e^0.2	e^0.4	0.579	0.550	0.608

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 three coefficient combinations we used to generate the data in this simulation study. We then calculated the odds ratio for the effect of sex given SNP and for the effect of SNP given sex. OR_sex|SNP0 refers to the odds ratio for the effect of sex (with female as the reference level and male equals to 1) given SNP = 0 for both coding schemes. For XCI (Clayton), ORsex|SNP2 refers to the odds ratio for the effect of sex given SNP = 2 (with female as the reference level); for eXCI (PLINK) coding, OR_sex|SNP1 refers to the odds ratio for the effect of sex given SNP = 1 (with female as the reference level). OR_SNP|M refers to the odds ratio for the effect of SNP, either comparing SNP = 0 with SNP = 2 in XCI or with SNP = 1 in eXCI 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 male (500 cases).