GEMMA Multivariate Linear Mixed Model
Calculate Omega matrices
Calculate Qi (inverse of Q) and log determinant of Q
Calculate Sigma_ee and Sigma_uu matrices
Calculate XHiY
Center a relatedness matrix, after Zhou's GEMMA function CenterMatrix
Eigendecomposition procedure for Vg and Ve
Calculate eigendecomposition and return ordered eigenvalues and eigenv...
gemma2
Calculate log likelihood
Perform expectation-maximization algorithm to infer Vg and Ve values f...
Stagger matrices within a larger, block-diagonal matrix
Update E
Update U matrix
Update V_e and V_g
Update B for restricted log likelihood
Fits a multivariate linear mixed effects model that uses a polygenic term, after Zhou & Stephens (2014) (<https://www.nature.com/articles/nmeth.2848>). Of particular interest is the estimation of variance components with restricted maximum likelihood (REML) methods. Genome-wide efficient mixed-model association (GEMMA), as implemented in the package 'gemma2', uses an expectation-maximization algorithm for variance components inference for use in quantitative trait locus studies.