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Code demonstrations:

MatrixEQTL::a.nocvrt Test that Matrix eQTL gives correct estimates for additive linear model. Homoscedastic case with no covariates.
MatrixEQTL::b.cvrt Test that Matrix eQTL gives correct estimates for additive linear model. Homoscedastic case with with covariates.
MatrixEQTL::c.weights Test that Matrix eQTL gives correct estimates for additive linear model. Heteroscedastic case with with covariates.
MatrixEQTL::d.ANOVA Test that Matrix eQTL gives correct estimates for ANOVA linear model. Heteroscedastic case with with covariates.
MatrixEQTL::e.interaction Test that Matrix eQTL gives correct estimates for linear model with genotype-covariate interaction. Heteroscedastic case with with covariates.
MatrixEQTL::sample.all Sample code for eQTL analysis of the toy data set.
MatrixEQTL::sample.cis Sample code for eQTL analysis of the toy data set with separate p-value thresholds and FDR estimation for cis- and trans-eQTLs.