Deprecate z transform in transformAssay (microbiome#584)

Signed-off-by: Daena Rys <[email protected]>
Co-authored-by: Tuomas Borman <[email protected]>

R/transformCounts.R

@@ -53,22 +53,8 @@
 #'
 #' \itemize{
 #' 
-#' \item 'alr': Additive log ratio (alr) transformation, please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.
-#' 
-#' \item 'chi.square': Chi square transformation, please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.
-#' 
-#' \item 'clr': Centered log ratio (clr) transformation, please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.
-#'
-#' \item 'frequency': Frequency transformation, please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.
-#' 
-#' \item 'hellinger':  Hellinger transformation, please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.
-#' 
-#' \item 'log':  Logarithmic transformation, please refer to 
+#' \item 'alr', 'chi.square', 'clr', 'frequency', 'hellinger', 'log', 'normalize', 'pa', 'rank', 'rclr'
+#' 'relabundance', 'rrank', 'standardize', 'total': please refer to 
 #' \code{\link[vegan:decostand]{decostand}} for details.
 #' 
 #' \item 'log10': log10 transformation can be used for reducing the skewness
@@ -82,34 +68,6 @@
 #' \deqn{log2 = \log_{2} x}{%
 #' log2 = log2(x)}
 #' where \eqn{x} is a single value of data.
-#' 
-#' \item 'normalize': Make margin sum of squares equal to one. Please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.
-#' 
-#' \item 'pa': Transforms table to presence/absence table. Please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.
-#'
-#' \item 'rank': Rank transformation, please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.
-#' 
-#' \item 'rclr':  Robust clr transformation, please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.
-#' 
-#' \item 'relabundance': Relative transformation (alias for 'total'), please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.
-#' 
-#' \item 'rrank': Relative rank transformation, please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.
-#' 
-#' \item 'standardize': Scale 'x' to zero mean and unit variance (alias for
-#' 'z'), please refer to \code{\link[vegan:decostand]{decostand}} for details.
-#' 
-#' \item 'total': Divide by margin total (alias for
-#' 'relabundance'), please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.
-#' 
-#' \item 'z': Z transformation (alias for 'standardize'),
-#' please refer to \code{\link[vegan:decostand]{decostand}} for details.
 #'
 #' }
 #'
@@ -312,6 +270,10 @@ setMethod("transformAssay", signature = c(x = "SummarizedExperiment"),
     MARGIN <- ifelse(MARGIN %in% c("samples", "columns", "col", 2), 2, 1)
     # Adjust method if mia-specific alias was used
     method <- ifelse(method == "relabundance", "total", method)
+
+    if (method == "z") {
+        .Deprecated(old="z", new="standardize")
+    }
     method <- ifelse(method == "z", "standardize", method)
 
     # If method is ALR, vegan drops one column/sample, because it is used