A novel phenotype imputation method with copula model

BMC Bioinformatics

Table 1 The type I error rates of genetic association tests with phenotypes imputed with different methods. (\(\alpha\)=0.05, 95\(\%\) confidence interval of \(\alpha\): (0.0362, 0.0638); heritability \(h^2=0;\) correlation of phenotypes \(\rho\) =0.5; 1000 replicated samples; sample size \(n=1000\))

Dist. \(^{1}\)	Association tests	Unimputed	PHENIX	PIM	C-MSE	C-(0–1)	C-QL
MVN	TATES	0.055	0.057	0.045	0.040	0.052	0.043
	MANOVA	0.049	0.036	0.043	0.038	0.037	0.042
	M-Phen	0.051	0.044	0.059	0.060	0.057	0.062
	AFC	0.055	0.046	0.037	0.043	0.058	0.061
	Tippel	0.049	0.061	0.055	0.056	0.049	0.044
MG	TATES	0.051	\(\mathbf {0.066}\)	\(\mathbf {0.071}\)	0.039	0.053	0.060
	MANOVA	0.054	\(\mathbf {0.065}\)	\(\mathbf {0.073}\)	0.051	0.047	0.043
	M-Phen	0.045	\(\mathbf {0.080}\)	\(\mathbf {0.075}\)	0.044	0.050	0.053
	AFC	0.055	\(\mathbf {0.065}\)	\(\mathbf {0.063}\)	0.047	0.056	0.059
	Tippel	0.050	\(\mathbf {0.074}\)	\(\mathbf {0.077}\)	0.060	0.054	0.039
Mixed	TATES	0.055	\(\mathbf {0.077}\)	\(\mathbf {0.085}\)	0.037	0.042	0.045
	MANOVA	0.049	\(\mathbf {0.079}\)	\(\mathbf {0.084}\)	0.056	0.052	0.061
	M-Phen	0.049	\(\mathbf {0.088}\)	\(\mathbf {0.079}\)	0.057	0.061	0.060
	AFC	0.036	\(\mathbf {0.068}\)	\(\mathbf {0.070}\)	0.048	0.060	0.054
	Tippel	0.048	\(\mathbf {0.090}\)	\(\mathbf {0.085}\)	0.056	0.061	0.053

\(^{1}\)Dist.: Phenotypes’ distributions; MVN: 7 phenotypes follow multivariate normal distribution (MVN); MG: 7 phenotypes follow multivariate gamma distribution; Mixed: 7 phenotypes follow a mixture of multivariate normal, beta, and gamma distributions
Bold values indicate inflated type I errors

ISSN: 1471-2105