Table 2.

Covariate coding schemes for examining the additive, dominance, gene–sex interaction, and sex effects under different assumptions of the X‐chromosome inactivation status and the choice of the baseline allele

Effect interpretation	Covariate notation	Non‐baseline allele	X‐chromosome inactivation (XCI) status	Coding schemes
				Females			Males
				$rr$	$rR$	$RR$	$r$	$R$
	$G_{A,R,I}$	$R$	Yes	0	0.5	1	0	1
Additive GA	$G_{A,r,I}$	$r$	Yes	1	0.5	0	1	0
$G_A$	$G_{A,R,N}$	$R$	No	0	1	2	0	1
	$G_{A,r,N}$	$r$	No	2	1	0	1	0
Dominance $G_D$	$G_D$	Either	Either	0	1	0	0	0
Gene–sex interaction	$G{S}_R$	$R$	Either	0	0	0	0	1
$GS=G_A\times S$	$G{S}_r$	$r$	Either	0	0	0	1	0
Sex $S$	$S$	Either	Either	0	0	0	1	1

Note: The subscripts $A$ and $D$ represent additive and dominance effects, $R$ or $r$ represents the non‐baseline allele of which we count the number of copies present in a genotype, and $I$ or $N$ denotes X‐chromosome inactivated or not inactivated.