R/calc_ll_bvlmm.R

In fboehm/pleiotropy: Likelihood ratio test to distinguish pleiotropy from linkage

#' Calculate log-likelihood for a bivariate LMM
#' 
#' @param yvec a vector of phenotype values, after removing NA values
#' @param Xmat a design matrix with needed number of rows
#' @param betahat estimate of beta; a vector of length 16
#' @param Vg 2 by 2 Vg matrix
#' @param Ve 2 by 2 Ve matrix
#' @param Kmat kinship matrix, for appropriate chromosome
#' @export

calc_ll_bvlmm <- function(yvec, Xmat, betahat, Vg, Ve, Kmat){
  n <- nrow(Kmat)
  In <- diag(1, n)
  mvtnorm::dmvnorm(yvec, 
                   mean = Xmat %*% betahat, 
                   sigma = Vg %x% Kmat + Ve %x% In, 
                   log = TRUE
                   )
}