R/transprob_ribo.R

In shimlab/riboHMM2: Analysis tool for Ribo-seq

#' transprob_ribo
#'
#' \code{transprob_ribo} creats the transition matrix for the hidden markov chain.
#'
#' @export
#' @param eL    see ...
#' @return      The transition matrix \code{A}
#'
#' @examples
#' null


transprob_ribo <- function(eL){
  M <- 21
  e_uORF <- 1/eL[1]
  l_uORF <- 3/(eL[2]-6)
  e_main <- 1/eL[3]
  l_main <- 3/(eL[4]-6)

  A <- diag(21)
  A <- cbind(0, A[, -21])
  A[1,1] <- 1 - e_uORF
  A[1,2] <- e_uORF
  A[7,5] <- 1 - l_uORF
  A[7,8] <- l_uORF
  A[11,11] <- 1 - e_main
  A[11,12] <- e_main
  A[17,15] <- 1 - l_main
  A[17,18] <- l_main
  A[21,21] <- 1

  return(A)
}