R/qc.R

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

qc <- function(trainingData, testData, geneList) {
  if (sum(is.na(testData) > 0)) {
    stop("Found missing values in the test data")
  }
  if (!is.null(trainingData)) {
    if (sum(is.na(trainingData) > 0)) {
      stop("Found missing values in the training data")
    }
    probe <- intersect(row.names(trainingData), row.names(testData))
    trainingData <- trainingData[match(probe, row.names(trainingData)), ]
    testData <- testData[match(probe, row.names(testData)), ]
  } else {
    probe <- row.names(testData)
  }
  for (i in seq_len(length(geneList))) {
    geneList[[i]] <- geneList[[i]][geneList[[i]] %in% probe]
  }
  rtlist <- list(testData = testData, geneList = geneList)
  if (!is.null(trainingData)) {
    rtlist <- c(rtlist, list(trainingData = trainingData))
  }
  return(rtlist)
}