#' init_generate
#'
#' \code{init_generate} generates a list of initial parameters
#' based on the ribo-seq.
#'
#' @export
#' @param df a list of dataset of ribo-seq
#' @param cutoff a scalar of cutoff point depending on histogram
#' @param r a scalar. Ratio of chians with uORF and non-uORF.
#' @return a list of initial parameters
#'
#' @examples
#' df <- uORF
#' init_generate(df, cutoff=10, r=4)
init_generate <- function(df, cutoff=10, r=4){
X <- RNA <-list()
E <- c()
num <- length(df)
for (i in 1:num){
X[[i]] <- df[[i]]$x
RNA[[i]] <- df[[i]]$RNA
E[i] <- df[[i]]$E
}
nx <- c()
for (i in 1:num){
nx <- c(nx, c(X[[i]]/E[i]))
}
m1 <- mean(nx[nx < 10])
m6 <- mean(nx[nx > 10])
init_m <- c(m1, rep(c(m6/3*4,m6,m6/3), 3),
m1, rep(c(m6/3*5,m6,m6/2), 3), m1)
trans_reg <- nx[nx > 10]
v <- m6^2/(var(trans_reg)-m6)
init_v <- rep(v, 21)
eL1 <- sum(nx < 10) /num/3
rho <- 1/eL1/(r+1)
rho_u <- r*rho
delta <- rho + rho_u
init <- list(v=init_v, m=init_m, trans=c(rho_u, rho, delta))
return(init)
}
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