R/update_trans.R

In shimlab/riboHMM2: Analysis tool for Ribo-seq

#' update_trans
#'
#' \code{update_trans} updates \code{trans} once.
#'
#' @export
#' @param num  number of chain
#' @param H    list of matrix H
#' @return     A vector of length 3, the updated paratemter and fval c(v'[k], m'[k], fval)
#'
#' @examples
#' df <- uORF[1:2]
#' X <- H <- list()
#' E <- c()
#' for (i in 1:2){
#'   X[[i]] <- df[[i]]$x
#'   RNA <- df[[i]]$RNA
#'   E[i]=df[[i]]$E;   trans=df[[i]]$trans;
#'   a=df[[i]]$v;      b=df[[i]]$v/df[[i]]$m
#'   la <- forwardAlg(X[[i]], RNA, trans, a, b, E[i])
#'   lb <- backwardAlg(X[[i]], RNA, trans, a, b, E[i])
#'   H[[i]] <- computeH(X[[i]], RNA, trans, a, b, E[i], la, lb)
#' }
#'
#' update_trans(length(df), H)

update_trans <- function(num, H){
  sH_it <- c(0,0,0,0,0)
  for (i in 1:num){
    sH_it <- sH_it + colSums(H[[i]])
  }
  denom1 <- sum(sH_it[1:3])
  denom2 <- sum(sH_it[4:5])
  trans <- sH_it[c(2,3,5)]/c(denom1,denom1,denom2)
  return(trans)
}