R/HiddenVarDecomp.R

In BASiCS: Bayesian Analysis of Single-Cell Sequencing data

# Used in BASiCS_VarianceDecomp
HiddenVarDecomp <- function(Chain)
{
  if (!is(Chain, "BASiCS_Chain")) {
    stop("'Chain' is not a BASiCS_Chain class object.")
  }

  N <- nrow(Chain@parameters$delta)
  q.bio <- ncol(Chain@parameters$delta)
  UniqueBatch <- colnames(Chain@parameters$theta)
  nBatch <- length(UniqueBatch)
  CellName <- colnames(Chain@parameters$s)

  if (nBatch > 1) {
    Theta <- matrixStats::rowMedians(Chain@parameters$theta)
  }
  else {
    Theta <- as.vector(Chain@parameters$theta)
  }

  # To store global values (uses median values across all cells)
  if("phi" %in% names(Chain@parameters)) {
    PhiS <- matrixStats::rowMedians(Chain@parameters$phi * Chain@parameters$s)
  }
  else {
    PhiS <- matrixStats::rowMedians(Chain@parameters$s)
  }

  Aux <- (1 / (PhiS * Chain@parameters$mu)) +
    Chain@parameters$delta *
    (Theta + 1)
  TechVarGlobal <- Theta / (Aux + Theta)
  BioVarGlobal <- (Chain@parameters$delta * (Theta + 1)) / (Aux + Theta)

  # To store batch specific values (in arrays)
  TechVarBatch <- array(0, dim = c(N, q.bio, nBatch))  # Technical
  BioVarBatch <- array(0, dim = c(N, q.bio, nBatch))  # Biological

  if (nBatch > 1) {
    for (Batch in seq_len(nBatch)) {
      SBatch <- Chain@parameters$s[, grep(UniqueBatch[Batch], CellName)]
      if("phi" %in% names(Chain@parameters)) {
        PhiBatch <- Chain@parameters$phi[, grep(UniqueBatch[Batch], CellName)]
        PhiSBatch <- matrixStats::rowMedians(PhiBatch * SBatch)
      }
      else {
        PhiSBatch <- matrixStats::rowMedians(SBatch)
      }

      Aux <- (1 / (PhiSBatch * Chain@parameters$mu)) +
              Chain@parameters$delta * (Chain@parameters$theta[, Batch] + 1)
      TechVarBatch[, , Batch] <-
        Chain@parameters$theta[,Batch] / (Aux + Chain@parameters$theta[, Batch])
      BioVarBatch[, , Batch] <- 
        (Chain@parameters$delta * (Chain@parameters$theta[, Batch] + 1)) /
        (Aux + Chain@parameters$theta[, Batch])
    }
  }

  if (nBatch > 1) {
    list(TechVarGlobal = TechVarGlobal,
         BioVarGlobal = BioVarGlobal,
         TechVarBatch = TechVarBatch,
         BioVarBatch = BioVarBatch)
  }
  else {
    list(TechVarGlobal = TechVarGlobal, BioVarGlobal = BioVarGlobal)
  }
}