Global and local ancestry estimates were used for complex trait association and admixture mapping by three group contributors. Thornton et al. [2013] performed an association analysis with a simulated DBP phenotype and SNP genotype data from the odd numbered chromosomes using the EMMAX method [Kang et al., 2010] that implements linear mixed model approach for association testing, accounting for both pedigree and global population substructures with an empirical covariance matrix. The authors compare their association analysis with EMMAX to a linear regression association analysis with the PLINK software [Purcell et al., 2007] where the top 10 PCs from a standard PCA were included as covariates.
