--- a
+++ b/R/DIscBIO-generic-pseudoTimeOrdering.R
@@ -0,0 +1,62 @@
+#' @title Pseudo-time ordering
+#' @description This function takes the exact output of exprmclust function and
+#'   construct Pseudo-time ordering by mapping all cells onto the path that
+#'   connects cluster centers.
+#' @param object \code{DISCBIO} class object.
+#' @param quiet if `TRUE`, suppresses intermediary output
+#' @param export if `TRUE`, exports order table to csv
+#' @param filename Name of the exported file (if `export=TRUE`)
+#' @importFrom TSCAN TSCANorder
+#' @return The DISCBIO-class object input with the kordering slot filled.
+setGeneric("pseudoTimeOrdering", function(
+    object,
+    quiet = FALSE,
+    export = FALSE,
+    filename = "Cellular_pseudo-time_ordering") {
+  standardGeneric("pseudoTimeOrdering")
+})
+
+#' @export
+#' @rdname pseudoTimeOrdering
+setMethod(
+  "pseudoTimeOrdering",
+  signature = "DISCBIO",
+  definition = function(object, quiet, export, filename) {
+    # ======================================================================
+    # Validating
+    # ======================================================================
+    ran_k <- length(object@kmeans$kpart) > 0
+    ran_m <- length(object@MBclusters) > 0
+    if (ran_k) {
+      Obj <- object@fdata
+      Names <- object@cpart
+      lpsmclust <- Exprmclust(Obj, K = 4, reduce = FALSE, cluster = Names)
+      lpsorder <- TSCANorder(lpsmclust)
+    } else if (ran_m) {
+      Obj <- object@fdata
+      Names <- names(object@MBclusters$clusterid)
+      lpsmclust <- object@MBclusters
+      lpsorder <- TSCANorder(lpsmclust)
+    } else {
+      stop("run clustexp before this pseudoTimeOrdering")
+    }
+    # ======================================================================
+    # Ordering
+    # ======================================================================
+    sampleNames <- colnames(Obj)
+    orderID <- lpsorder
+    order <- seq_len(length(lpsorder))
+    orderTable <- data.frame(order, orderID)
+    if (export) write.csv(orderTable, file = paste0(filename, ".csv"))
+    if (!quiet) print(orderTable)
+    FinalOrder <- orderTable[match(sampleNames, orderTable$orderID), ]
+    out_order <- FinalOrder[, 1]
+    names(out_order) <- names(Names)
+    if (ran_k) {
+      object@kordering <- out_order
+    } else if (ran_m) {
+      object@MBordering <- out_order
+    }
+    return(object)
+  }
+)