R/CovR.parallel.R

In haowulab/TRESS: Toolbox for mRNA epigenetics sequencing analysis

CovR.parallel <- function(mat, sf, model, variable,
                          Coef, phi, theta){
  #### Calculate Cov(R) in parallel
  X = mat[,seq(1, ncol(mat), 2)]
  sx = sf[seq(1, ncol(mat), 2)]
  Y = mat[, seq(2, ncol(mat), 2)]
  sy = sf[seq(2, ncol(mat), 2)]
  D = model.matrix(model, variable)
  # res = mclapply(1:nrow(mat), iCovR,
  #                X, Y, sx, sy, D,
  #                Coef, phi, theta,
  #                mc.cores = 2 #max(1, detectCores() - 1)
  #                )
  res = mclapply(seq_len(nrow(mat)), iCovR,
                 X, Y, sx, sy, D,
                 Coef, phi, theta,
                 mc.cores = 2
                 )
  R = matrix(NA, nrow = nrow(mat), ncol = ncol(D))
  Cov = vector("list", length = nrow(mat))
  #for (i in 1:length(res)) {
  for (i in seq_len(length(res))) {
    R[i, ] = res[[i]]$R
    Cov[[i]] = res[[i]]$Cov
  }
  colnames(R) = colnames(D)
  #########
  return(list(Coef = R, Cov = Cov))
}