--- a/w4mclassfilter_wrapper.R	Fri Mar 02 08:29:53 2018 -0500
+++ b/w4mclassfilter_wrapper.R	Mon Sep 03 22:28:03 2018 -0400
@@ -102,18 +102,31 @@
 ## -----------------------------
 my_w4m_filter_imputation <- if (transformation == "log10") {
   function(m) {
+    if (!is.matrix(m))
+      stop("Cannot impute and transform data - the supplied data is not in matrix form")
+    if (nrow(m) == 0)
+      stop("Cannot impute and transform data - data matrix has no rows")
+    if (ncol(m) == 0)
+      stop("Cannot impute and transform data - data matrix has no columns")
     suppressWarnings(
       # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step
       m <- log10(m)
     )
-    # replace NaN values with zero
-    m[is.nan(m)] <- 0
-    # replace NA values with zero
-    m[is.na(m)] <- 0
-    # replace negative values with zero, if applicable (It should never be applicable!)
-    m[m<0] <- 0
-    # return matrix as the result
-    return (m)
+    return ( w4m_filter_imputation(m) )
+  }
+} else if (transformation == "log2") {
+  function(m) {
+    if (!is.matrix(m))
+      stop("Cannot impute and transform data - the supplied data is not in matrix form")
+    if (nrow(m) == 0)
+      stop("Cannot impute and transform data - data matrix has no rows")
+    if (ncol(m) == 0)
+      stop("Cannot impute and transform data - data matrix has no columns")
+    suppressWarnings(
+      # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step
+      m <- log2(m)
+    )
+    return ( w4m_filter_imputation(m) )
   }
 } else {
   # use the method from the w4mclassfilter class