R/MakeGSoptions.R

In DMRMark: DMR Detection by Non-Homogeneous Hidden Markov Model from Methylation Array Data

MakeGSoptions <- function(pi0 = c(100,100,5,5),
                          cmu0 = c(11.5, 11.5, 8, 8),
                          theta0 = c(-3,2),
                          mu0 = matrix(c(-2,2,2,-2),2, byrow = TRUE),
                          kappa0 = c(50,50,5,5),
                          nu0 = rep(4,2),
                          A0 = array(rep(c(2,0.8,0.8,4),2),dim = c(2,2,2)),
                          alpha12N = rep(40,3),
                          beta12N = rep(60,3),
                          D_mu = rep(-2,2),
                          chi_alpha = 0.2,
                          burnin = 500,
                          nsamples = 100,
                          sampleSep = 10,
                          onHMM = TRUE,
                          track = FALSE,
                          verbose = FALSE) {
  
  opts <- list(pi0 = pi0,
               cmu0 = cmu0,
               theta0 = theta0,
               mu0 = mu0,
               kappa0 = kappa0,
               nu0 = nu0,
               A0 = A0,
               alpha12N = alpha12N,
               beta12N = beta12N,
               D_mu = D_mu,
               chi_alpha = chi_alpha,
               burnin = burnin,
               nsamples = nsamples,
               sampleSep = sampleSep,
               onHMM = onHMM,
               track = track,
               verbose = verbose)
  
  return(opts)
}