--- a
+++ b/R/getStdiz.R
@@ -0,0 +1,40 @@
+#' @name getStdiz
+#' @title Get standardized omics data
+#' @description This function prepare standardized data for generating heatmap. Omics data, especially for expression, should be centered or scaled or z-scored (both centered and scaled). Generally, DNA methylation beta matrix and somatic mutation (0 and 1 binary matrix) should not be normalized. This function also provides an argument of `halfwidth` for continuous omics data; such argument is used to truncate the 'extremum' after normalization; specifically, normalized values that exceed the halfwidth boundaries will be replaced by the halfwidth, which is vary useful to map colors in heatmap.
+#' @param data A list of data.frame or matrix storing raw multiple omics data with rows for features and columns for samples.
+#' @param halfwidth A numeric vector to assign marginal cutoff for truncating values in data; 1 by default.
+#' @param centerFlag A logical vector to indicate if each subdata should be centered; TRUE by default.
+#' @param scaleFlag A logical vector to indicate if each subdata should be scaled; TRUE by default.
+#' @export
+#' @return A standardized data.frame containing multi-omics data.
+#' @examples # There is no example and please refer to vignette.
+getStdiz <- function(data       = NULL,
+                     halfwidth  = rep(1, length(data)),
+                     centerFlag = rep(TRUE, length(data)),
+                     scaleFlag  = rep(TRUE, length(data))) {
+
+  # check data
+  if(is.null(names(data))){
+    names(data) <- sprintf("dat%s", 1:length(data))
+  }
+
+  n_dat <- length(data)
+  if(n_dat > 6){
+    stop("current version of MOVICS can support up to 6 datasets.")
+  }
+  if(n_dat < 2){
+    stop('current verision of MOVICS needs at least 2 omics data.')
+  }
+
+  outdata <- list()
+  for (i in 1:n_dat) {
+    tmp <- t(scale(t(data[[i]]), center = centerFlag[i], scale = scaleFlag[i]))
+    if (!is.na(halfwidth[i])) {
+      tmp[tmp > halfwidth[i]] = halfwidth[i]
+      tmp[tmp < (-halfwidth[i])] = -halfwidth[i]
+    }
+    outdata[[names(data)[i]]] <- tmp
+  }
+
+  return(outdata)
+}