R/data_prep_s2.R

In compbiomed/ASSIGN: Adaptive Signature Selection and InteGratioN (ASSIGN)

# only the geneList and test data is available
data_prep_s2 <- function(geneList, anchorGenes, testData, theta0, theta1) {
  S <- matrix(0, nrow = nrow(testData), ncol = length(geneList))

  for (i in seq_len(length(geneList))) {
    tmp <- match(geneList[[i]], row.names(testData))
    tmp <- tmp[!is.na(tmp)]
    S[tmp, i] <- 1
  }

  #Check for anchor Genes
  if (!is.null(anchorGenes)) {
    for (j in seq_len(length(names(anchorGenes)))) {
      #if an anchor gene is not in the geneList
      if (length(intersect(geneList[[j]], anchorGenes[[j]])) != length(anchorGenes[[j]])) {
        #FAIL with error message
        stop("All anchor genes must be listed in the geneList")
      }
    }
  }

  rownames(S) <- row.names(testData)
  colnames(S) <- names(geneList)

  S1 <- S[apply(S, 1, sum) != 0, ]
  S2 <- stats::runif(length(S1), 0, 1); dim(S2) <- dim(S1)
  rownames(S2) <- rownames(S1); colnames(S2) <- colnames(S1)
  test <- testData[apply(S, 1, sum) != 0, ]

  B <- stats::runif(NROW(S1), 0, 1)
  Pi_matrix <- as.matrix(ifelse(S1 == 0, theta0, theta1))

  #change the Pi_matrix values for the anchor genes to 1
  if (!is.null(anchorGenes)) {
    for (j in seq_len(length(names(anchorGenes)))) {
      for (k in seq_len(length(anchorGenes[[j]]))) {
        Pi_matrix[anchorGenes[[j]][k], j] <- 1
      }
    }
  }

  return(list(testData_sub = test, Delta_matrix = S1, Pi_matrix = Pi_matrix,
              S_matrix = S2, B_vector = B))
}