--- a
+++ b/R/DIscBIO-generic-comptSNE.R
@@ -0,0 +1,68 @@
+#' @title Computing tSNE
+#' @description This function is used to compute the t-Distributed Stochastic
+#'   Neighbor Embedding (t-SNE).
+#' @param object \code{DISCBIO} class object.
+#' @param rseed Random integer to to yield reproducible maps across different
+#' runs
+#' @param max_iter maximum number of iterations to perform.
+#' @param epoch The number of iterations in between update messages.
+#' @param quiet if `TRUE`, suppresses intermediate output
+#' @param ... other parameters to be passed to `tsne::tsne`
+#' @importFrom tsne tsne
+#' @importFrom stats as.dist cor
+#' @return The DISCBIO-class object input with the tsne slot filled.
+#' @examples
+#' sc <- DISCBIO(valuesG1msTest) # changes signature of data
+#' sc <- Clustexp(sc, cln = 2) # data must be clustered before plottin
+#' sc <- comptSNE(sc, max_iter = 30)
+#' head(sc@tsne)
+#'
+setGeneric(
+  name = "comptSNE",
+  def = function(
+      object, rseed = NULL, max_iter = 5000, epoch = 500, quiet = FALSE, ...) {
+    standardGeneric("comptSNE")
+  }
+)
+
+#' @rdname comptSNE
+#' @export
+setMethod(
+  f = "comptSNE",
+  signature = "DISCBIO",
+  definition = function(object, rseed, max_iter, epoch, quiet, ...) {
+    # ======================================================================
+    # Validating
+    # ======================================================================
+    ran_k <- length(object@kmeans$kpart) > 0
+    ran_m <- length(object@MBclusters) > 0
+    if (ran_k) {
+      di <- dist.gen(as.matrix(object@distances))
+    } else if (ran_m) {
+      di <- dist.gen(as.matrix(t(object@fdata)))
+    } else {
+      stop("run clustexp before comptSNE")
+    }
+    # ======================================================================
+    # Computing
+    # ======================================================================
+    set.seed(rseed)
+    if (quiet) {
+      ts <- suppressMessages(
+        tsne(di, max_iter = max_iter, epoch = epoch, ...)
+      )
+    } else {
+      message("This function may take time")
+      ts <- tsne(di, max_iter = max_iter, epoch = epoch, ...)
+    }
+    # ======================================================================
+    # Filling output
+    # ======================================================================
+    if (ran_k) {
+      object@tsne <- as.data.frame(ts)
+    } else if (ran_m) {
+      object@MBtsne <- as.data.frame(ts)
+    }
+    return(object)
+  }
+)