R/afr_va.R

In ericwatt/eapath: Computational Models for Estrogen and Androgen Receptor Activity

#' Function minimized in model
#'
#' \code{afr_va} is the function passed to \code{optim} in \code{er_model}.
#'
#' @param x x
#' @param A A matrix
#' @param nassay integer
#' @param nreceptor integer
#' @param pathway character flag, "ER" or "AR"
#' @param penalty_method character
#' @param alpha numeric
#'
#' @return eret
afr_va <- function(x, A, nassay, nreceptor, pathway, penalty_method, alpha) {
  Ameas <- A[,1]
  F <- as.matrix(A[,2:(nreceptor+1)])
  R <- matrix(nrow=nreceptor,ncol=1)
  R[] <- x
  Apred <- F%*%R
  w <- vector(mode="numeric",length=nassay)
  w[] <- 1

  if (pathway == "ER"){
    w[1] <- 1/3
    w[2] <- 1/3
    w[3] <- 1/3
    w[4] <- 1/6
    w[5] <- 1/6
    w[6] <- 1/6
    w[7] <- 1/6
    w[8] <- 1/6
    w[9] <- 1/6
    w[10] <- 1/2
    w[11] <- 1/2
    w[12] <- 1/2
    w[13] <- 1/2
    w[14] <- 1/2
    w[15] <- 1/2
    w[16] <- 1/1
    w[17] <- 1/2
    w[18] <- 1/2
  }
  #w[] <- 1

  eret <- 0
  bot <- 0
  top <- 0
  mask <- Ameas
  mask[] <- 1
  mask[is.na(Ameas)] <- 0
  for(i in 1:nassay) {
    if(mask[i]==1) {
      top <- top + w[i] * (Apred[i]-Ameas[i])**2
      bot <- bot + w[i]
    }
  }
  eret <- top/bot/sum(mask) + penalty(R, pathway = pathway, alpha = alpha, penalty_method = penalty_method)
  return(eret)
}