R/makeA.R

In matthewwolak/nadiv: (Non)Additive Genetic Relatedness Matrices

#' Creates the additive genetic relationship matrix
#' 
#' This returns the additive relationship matrix in sparse matrix format.
#' 
#' Missing parents (e.g., base population) should be denoted by either 'NA',
#' '0', or '*'.
#' 
#' Used as a support function to \code{\link{makeD}}.
#' 
#' See function \code{\link{makeAinv}} for directly obtaining the inverse of
#' the additive genetic relationship matrix.
#' 
#' @param pedigree A pedigree where the columns are ordered ID, Dam, Sire
#'
#' @return Returns A, or the numerator relationship matrix, in sparse 
#'   matrix form.
#' @author \email{matthewwolak@@gmail.com}
#' @seealso \code{\link{makeD}}, \code{\link{makeS}}
#' @examples
#' 
#'  makeA(Mrode2)
#' 
#' @export
makeA <- function(pedigree)
{
  nPed <- numPed(pedigree)
#  sqrtDinv <- makeDiiF(nPed)$D
#    sqrtDinv@x <- sqrt(1 / sqrtDinv@x)
  A <- as(tcrossprod(solve(Diagonal(x = sqrt(1 / makeAinv(pedigree)$dii),
           n = nrow(nPed)) %*% makeTinv(nPed))),
         "symmetricMatrix")
    A@Dimnames <- list(as.character(pedigree[, 1]),
			as.character(pedigree[, 1]))
 A
}