diff withinvariation-26603602a823/transformation_script.R @ 0:5086ad0c0992 draft default tip

Uploaded v0.4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/withinvariation-26603602a823/transformation_script.R	Fri May 05 05:04:36 2017 -0400
@@ -0,0 +1,73 @@
+## Etienne Thevenot
+## W4M Core Development Team
+## [e-mail]
+## 2015-04-25
+
+transformF <- function(datMN,
+                       metC) {
+    
+    ## options
+    
+    optStrAsFacL <- options()[["stringsAsFactors"]]
+    options(stringsAsFactors = FALSE)
+    
+    ## checking		     
+    
+    if(length(which(datMN < 0))) {
+        cat("\nThe 'dataMatrix' contains negative values\n")
+        sink()
+        stop("The 'dataMatrix' contains negative values", call. = FALSE)
+    }
+    
+    ## 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(datMN == 0))
+    cat("\nZero values in the 'dataMatrix': ",
+        zerN,
+        " (",
+        round(zerN / cumprod(dim(datMN))[2] * 100),
+        "%)\n",
+        sep="")
+    
+    ## transformation
+    
+    switch(metC,
+           log2 = {
+
+               cat("\n'log2' transformation\n", sep="")
+
+               trfMN <- log2(1 + datMN)
+
+           },
+           log10 = {
+
+               cat("\n'log10' transformation\n", sep="")
+
+               trfMN <- log10(1 + datMN)
+
+           },
+           sqrt = {
+
+               cat("\n'Square root' transformation\n", sep="")
+               
+               trfMN <- sqrt(datMN)
+
+
+           }) ## end of method
+
+
+    ## returning
+
+    options(stringsAsFactors=optStrAsFacL)
+
+    return(trfMN)
+
+} ## end of transformF
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