MultiPhen is an R package available from CRAN (http://cran.r-project.org/web/packages/MultiPhen/MultiPhen.pdf) for the R software (http://www.r-project.org/) [12]. The test for association is a likelihood ratio test (LRT) for model fit, testing whether all regression coefficients in the model are jointly significantly different from zero. We analyzed the simulation data using the mPhen function, specifying the genotype data, phenotype data and JointModel = TRUE. This results in a p-value per trait and a p-value for the LRT. The latter was extracted from the output.
