R/data_prep_s1.R

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

# training data and label are available, but geneList is not available.

data_prep_s1 <- function(n_sigGene, trainingData, testData, trainingLabel,
                         geneList, anchorGenes, excludeGenes, theta0,
                         theta1, pctUp = 0.5, iter = 500, burn_in = 100,
                         progress_bar = TRUE) {
  if (is.null(geneList)) {
    geneSelection <- bayes.gene.selection(n_sigGene, dat = trainingData,
                                          trainingLabel, iter = iter,
                                          burn_in = burn_in, sigmaZero = 0.1,
                                          sigmaNonZero = 1, alpha_tau = 1,
                                          beta_tau = 0.01, p = 0.01,
                                          pctUp = pctUp,
                                          anchorGenes = anchorGenes,
                                          excludeGenes = excludeGenes,
                                          progress_bar = progress_bar)
    diffGeneList <- geneSelection$diffGeneList
  } else {
    diffGeneList <- geneList
  }

  #Add anchor genes to list if they aren't in there
  if (!is.null(anchorGenes)) {
    for (j in seq_len(length(names(anchorGenes)))) {
      #if an anchor gene is not in the diffGeneList
      if (length(intersect(diffGeneList[[j]], anchorGenes[[j]])) != length(anchorGenes[[j]])) {
        #for each anchor gene, if it's not there, replace last gene
        replaced <- 0
        for (k in seq_len(length(anchorGenes[[j]]))) {
          if (!(anchorGenes[[j]][k] %in% diffGeneList[[j]])) {
            diffGeneList[[j]][length(diffGeneList[[1]]) - replaced] <- anchorGenes[[j]][k]
            replaced <- replaced + 1
          }
        }
      }
    }
  }

  #Remove exclude genes if they are in there
  if (!is.null(excludeGenes)) {
    for (j in seq_len(length(names(excludeGenes)))) {
      #if an exclude gene is in geneList
      if (length(intersect(diffGeneList[[j]], excludeGenes[[j]])) != 0) {
        #remove any exclude genes
        diffGeneList[[j]] <- diffGeneList[[j]][!(diffGeneList[[j]] %in% excludeGenes[[j]])]
      }
    }
  }

  signature <- geneMatch_sub2(dat = trainingData, diffGeneList, trainingLabel)

  tmp1 <- match(unique(unlist(diffGeneList)), row.names(trainingData))

  trainingBaseline_sub <- rowMeans(trainingData[tmp1, unique(unlist(trainingLabel$control))])
  trainingData_sub <- trainingData[tmp1, ]
  testData_sub <- testData[tmp1, ]

  if (is.null(geneList)) {
    Pi_matrix <- geneSelection$prior_p[tmp1, ]
    Pi_matrix <- Pi_matrix * signature$Delta_matrix #??Do we force the non-signatue genes to be 0??
    Pi_matrix <- theta0 + Pi_matrix * theta1
  } else {
    Pi_matrix <- signature$Delta_matrix
    Pi_matrix <- theta0 + Pi_matrix * 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], names(anchorGenes)[j]] <- 1
      }
    }
  }
  return(list(trainingBaseline_sub = trainingBaseline_sub,
              S_matrix = signature$S_matrix,
              Delta_matrix = signature$Delta_matrix, Pi_matrix = Pi_matrix,
              trainingData_sub = trainingData_sub, testData_sub = testData_sub,
              diffGeneList = diffGeneList))
}