--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/transformation_script.R	Fri Jul 29 12:11:01 2016 -0400
@@ -0,0 +1,85 @@
+## Etienne Thevenot
+## W4M Core Development Team
+## etienne.thevenot@cea.fr
+## 2015-04-25
+
+transformF <- function(datMN,
+                       metC) {
+
+    ## options
+
+    optStrAsFacL <- options()[["stringsAsFactors"]]
+    options(stringsAsFactors = FALSE)
+
+    ## transformation
+
+    switch(metC,
+           log2 = {
+
+               cat("\n'log2' transformation\n", sep="")
+
+               if(length(which(datMN < 0)))
+                   stop("The 'dataMatrix' contains negative values")
+
+               zerMN <- datMN == 0
+
+               ## Number of missing values
+               nasN <- length(which(is.na(datMN)))
+               cat("\nMissing values in the 'dataMatrix': ",
+                   nasN,
+                   " (",
+                   round(nasN / cumprod(dim(datMN))[2] * 100),
+                   "%)\n",
+                   sep="")
+
+               ## Number of zero values
+               zerN <- length(which(zerMN))
+               cat("\nZero values in the 'dataMatrix': ",
+                   zerN,
+                   " (",
+                   round(zerN / cumprod(dim(datMN))[2] * 100),
+                   "%)\n",
+                   sep="")
+
+               trfMN <- log2(1 + datMN)
+
+           },
+           log10 = {
+
+               cat("\n'log10' transformation\n", sep="")
+
+               if(length(which(datMN < 0)))
+                   stop("The 'dataMatrix' contains negative values")
+
+               zerMN <- datMN == 0
+
+               ## Number of missing values
+               nasN <- length(which(is.na(datMN)))
+               cat("\nMissing values in the 'dataMatrix': ",
+                   nasN,
+                   " (",
+                   round(nasN / cumprod(dim(datMN))[2] * 100),
+                   "%)\n",
+                   sep="")
+
+               ## Number of zero values
+               zerN <- length(which(zerMN))
+               cat("\nZero values in the 'dataMatrix': ",
+                   zerN,
+                   " (",
+                   round(zerN / cumprod(dim(datMN))[2] * 100),
+                   "%)\n",
+                   sep="")
+
+               trfMN <- log10(1 + datMN)
+
+           }) ## end of 'log10' method
+
+
+    ## returning
+
+    options(stringsAsFactors=optStrAsFacL)
+
+    return(trfMN)
+
+} ## end of transformF