diff --git a/R/deprecate.R b/R/deprecate.R
index 1478ff630..e7de57ff7 100644
--- a/R/deprecate.R
+++ b/R/deprecate.R
@@ -104,54 +104,3 @@ loadFromHumann <- function(...) {
                             " Use 'importHUMAnN' instead."))
     importHUMAnN(...)
 }
-
-#' @rdname deprecate
-#' @export
-setGeneric("subsetSamples", signature = "x",
-            function(x, ...)
-                standardGeneric("subsetSamples"))
-
-#' @rdname deprecate
-#' @export
-setMethod("subsetSamples", signature = "SummarizedExperiment",
-            function(x, ...){
-                .Deprecated(msg = paste0("subsetSamples is deprecated. Please ",
-                                        "use '[]' for subsetting instead."))
-                subset_args <- .get_subset_args(x, ...)
-                x[subset_args$columns,subset_args$rows]
-            }
-)
-
-#' @rdname deprecate
-#' @export
-setGeneric("subsetFeatures", signature = "x",
-            function(x, ...)
-                standardGeneric("subsetFeatures"))
-
-#' @rdname deprecate
-#' @export
-setMethod("subsetFeatures", signature = "SummarizedExperiment",
-            function(x, ...){
-                .Deprecated(msg = paste0("subsetFeatures is deprecated. Please",
-                                        " use '[]' for subsetting instead."))
-                subset_args <- .get_subset_args(x, ...)
-                x[subset_args$rows, subset_args$columns]
-            }
-)
-
-#' @rdname deprecate
-#' @export
-setGeneric("subsetTaxa", signature = "x",
-            function(x, ...)
-                standardGeneric("subsetTaxa"))
-
-#' @rdname deprecate
-#' @export
-setMethod("subsetTaxa", signature = "SummarizedExperiment",
-            function(x, ...){
-                .Deprecated(msg = paste0("subsetFeatures is deprecated. Please",
-                                        " use '[]' for subsetting instead."))
-                subset_args <- .get_subset_args(x, ...)
-                x[subset_args$rows, subset_args$columns]
-            }
-)
diff --git a/R/subset.R b/R/subset.R
index b045e0b9c..e2026103d 100644
--- a/R/subset.R
+++ b/R/subset.R
@@ -1,3 +1,16 @@
+#' @export
+setGeneric("subsetSamples", signature = "x",
+           function(x, ...)
+               standardGeneric("subsetSamples"))
+#' @export
+setGeneric("subsetFeatures", signature = "x",
+           function(x, ...)
+               standardGeneric("subsetFeatures"))
+#' @export
+setGeneric("subsetTaxa", signature = "x",
+           function(x, ...)
+               standardGeneric("subsetTaxa"))
+
 .get_subset_args <- function(x, subset = NULL, select = NULL, ...){
     rows <- subset
     columns <- select
@@ -9,3 +22,32 @@
     }
     return(list(rows = rows, columns = columns))
 }
+
+#' @export
+setMethod("subsetSamples", signature = "SummarizedExperiment",
+          function(x, ...){
+              .Deprecated(msg = paste0("subsetSamples is deprecated. Please ",
+                                       "use '[]' for subsetting instead."))
+              subset_args <- .get_subset_args(x, ...)
+              x[subset_args$columns,subset_args$rows]
+          }
+)
+
+#' @export
+setMethod("subsetFeatures", signature = "SummarizedExperiment",
+          function(x, ...){
+              .Deprecated(msg = paste0("subsetFeatures is deprecated. Please",
+                                       " use '[]' for subsetting instead."))
+              subset_args <- .get_subset_args(x, ...)
+              x[subset_args$rows, subset_args$columns]
+          }
+)
+
+#' @export
+setMethod("subsetTaxa", signature = "SummarizedExperiment",
+          function(x, ...){
+              .Deprecated(msg = paste0("subsetFeatures is deprecated. Please",
+                                       " use '[]' for subsetting instead."))
+              subsetFeatures(x, ...)
+          }
+)
diff --git a/man/deprecate.Rd b/man/deprecate.Rd
index b3cea6dca..31d5fa706 100644
--- a/man/deprecate.Rd
+++ b/man/deprecate.Rd
@@ -14,12 +14,6 @@
 \alias{loadFromMothur}
 \alias{loadFromMetaphlan}
 \alias{loadFromHumann}
-\alias{subsetSamples}
-\alias{subsetSamples,SummarizedExperiment-method}
-\alias{subsetFeatures}
-\alias{subsetFeatures,SummarizedExperiment-method}
-\alias{subsetTaxa}
-\alias{subsetTaxa,SummarizedExperiment-method}
 \title{These functions will be deprecated. Please use other functions instead.}
 \usage{
 cluster(x, ...)
@@ -45,18 +39,6 @@ loadFromMothur(...)
 loadFromMetaphlan(...)
 
 loadFromHumann(...)
-
-subsetSamples(x, ...)
-
-\S4method{subsetSamples}{SummarizedExperiment}(x, ...)
-
-subsetFeatures(x, ...)
-
-\S4method{subsetFeatures}{SummarizedExperiment}(x, ...)
-
-subsetTaxa(x, ...)
-
-\S4method{subsetTaxa}{SummarizedExperiment}(x, ...)
 }
 \arguments{
 \item{x}{A