From dd72584db6760a303030924f6da86f79424046e3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
Date: Wed, 27 May 2026 10:26:07 -0700
Subject: [PATCH] Use new BiocGenerics::transform() with new signature

---
 DESCRIPTION                   |  2 +-
 NAMESPACE                     |  2 +-
 R/AllGenerics.R               |  8 --------
 R/flowFrame-accessors.R       | 14 +++++++-------
 R/flowSet-accessors.R         | 18 ++++++++++--------
 docs/reference/transform.html |  4 ++--
 man/transform.Rd              |  4 ++--
 src/inPolygon.cpp             |  2 +-
 8 files changed, 24 insertions(+), 30 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index faa564aa..323d3b30 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -17,7 +17,7 @@ Depends:
     R (>= 3.0.2)
 Imports:
     Biobase,
-    BiocGenerics (>= 0.29.2),
+    BiocGenerics (>= 0.59.5),
     grDevices,
     graphics,
     methods,
diff --git a/NAMESPACE b/NAMESPACE
index 2319da5e..0d2a795f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -118,7 +118,6 @@ export(squareroot)
 export(summarizeFilter)
 export(tail)
 export(timeFilter)
-export(transform)
 export(transformList)
 export(transformReference)
 export(transform_gate)
@@ -272,6 +271,7 @@ importFrom(BiocGenerics,ncol)
 importFrom(BiocGenerics,nrow)
 importFrom(BiocGenerics,sort)
 importFrom(BiocGenerics,toTable)
+importFrom(BiocGenerics,transform)
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,coolcat)
 importFrom(cytolib,cytolib_LdFlags)
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index 7ed8c37b..318e6670 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -89,14 +89,6 @@ setGeneric("identifier<-",function(object,value)
 
 
 
-## ===========================================================================
-## Generic for transformation (already S3 in base)
-## ---------------------------------------------------------------------------
-#' @export
-setGeneric("transform")
-
-
-
 ## ===========================================================================
 ## Generics for split and Subset (split is already S3 in base)
 ## ---------------------------------------------------------------------------
diff --git a/R/flowFrame-accessors.R b/R/flowFrame-accessors.R
index 54f8d5c6..bf11ad20 100644
--- a/R/flowFrame-accessors.R
+++ b/R/flowFrame-accessors.R
@@ -836,7 +836,7 @@ setMethod("compensate",
 #' 
 #' @name transform
 #' @aliases transform,flowFrame-method transform,flowSet-method
-#' @param _data a flowFrame or flowSet object
+#' @param x a flowFrame or flowSet object
 #' @param translist a transformList object
 #' @param ... other arguments. e.g. `FL1-H` = myFunc(`FL1-H`)
 #' 
@@ -861,6 +861,7 @@ setMethod("compensate",
 #' 
 #' 
 #' @export
+#' @importFrom BiocGenerics transform
 # 
 # We are also making sure that the values of the dynamic range in the
 # parameters slot are transformed accordingly. Note that this does not
@@ -869,8 +870,8 @@ setMethod("compensate",
 # The `FL1-H` = myFunc(`FL1-H` ) form is not intended to be used in programmatic way
 # since use non-standard evalution could fail to find 'myFunc' definition. 
 setMethod("transform",
-          signature=signature(`_data`="flowFrame"),
-          definition=function(`_data`, translist, ...)
+          signature=signature(x="flowFrame"),
+          definition=function(x, translist, ...)
       {
         
           if(!(missing(translist))){
@@ -881,18 +882,17 @@ setMethod("transform",
               err_msg <- paste(err_msg, "!Please make sure the unnamed argument is a valid 'transformList' object!")
               stop(err_msg)
             }else
-                return(translist %on% `_data`)
+                return(translist %on% x)
           }else# dispach to .transform for named argument, assuming it is like `FSC-H`=asinhTrans(`FSC-H`) 
-            .transform(`_data`, ...)
+            .transform(x, ...)
    
       })
 
 #' take formal of transform(fs, `FSC-H`=asinhTrans(`FSC-H`))
 #' which do the lazy evaluation
 #' @noRd
-.transform <- function(`_data`, ...){
+.transform <- function(x, ...){
       e <- substitute(list(...))
-      x <- `_data`
       par <- parameters(x)
       ranges <- range(x)
       tranges <- as.matrix(transform(as.data.frame(ranges),...))
diff --git a/R/flowSet-accessors.R b/R/flowSet-accessors.R
index a3a49360..ec24d354 100644
--- a/R/flowSet-accessors.R
+++ b/R/flowSet-accessors.R
@@ -427,19 +427,20 @@ setMethod("compensate",
 ## Transformation methods
 ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 #' @export
+#' @importFrom BiocGenerics transform
 setMethod("transform",
-		signature=signature(`_data`="flowSet"),
-		definition=function(`_data`, translist, ...)
+		signature=signature(x="flowSet"),
+		definition=function(x, translist, ...)
 		{
 		  if(missing(translist))
-		    fsApply(`_data`,transform, ...)
+		    fsApply(x,transform, ...)
 		  else if(is(translist, "transformList"))
-			  fsApply(`_data`,transform, translist = translist, ...)
+			  fsApply(x,transform, translist = translist, ...)
 		  else if(is(translist, "list")){
-		    sns <- sampleNames(`_data`)
+		    sns <- sampleNames(x)
 		    if(!setequal(sns, names(translist)))
 		      stop("names of 'translist' must be consistent with flow data!")
-		    fs <- copyFlowSet(`_data`)
+		    fs <- copyFlowSet(x)
 		    for(sn in sns)
 		      fs[[sn]] <- transform(fs[[sn]], translist[[sn]])
 		    fs
@@ -449,8 +450,9 @@ setMethod("transform",
 		})
 
 #' @export
+#' @importFrom BiocGenerics transform
 setMethod("transform",
-		signature=signature(`_data`="missing"),
+		signature=signature(x="missing"),
 		definition=function(...)
 		{
 			funs <- list(...)
@@ -752,4 +754,4 @@ flowSet_to_list <- function(fs){
   frs <- lapply(1:length(fs), function(idx) {fs[[idx]]})
   names(frs) <- sampleNames(fs)
   frs
-}
\ No newline at end of file
+}
diff --git a/docs/reference/transform.html b/docs/reference/transform.html
index d9fab1a7..728d6a99 100644
--- a/docs/reference/transform.html
+++ b/docs/reference/transform.html
@@ -132,13 +132,13 @@ <h1>Transform a flowFrame or flowSet</h1>
     </div>
 
     <pre class="usage"><span class='co'># S4 method for flowFrame</span>
-<span class='fu'>transform</span>(<span class='no'>`_data`</span>, <span class='no'>translist</span>, <span class='no'>...</span>)</pre>
+<span class='fu'>transform</span>(<span class='no'>`x`</span>, <span class='no'>translist</span>, <span class='no'>...</span>)</pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
-      <th>_data</th>
+      <th>x</th>
       <td><p>a flowFrame or flowSet object</p></td>
     </tr>
     <tr>
diff --git a/man/transform.Rd b/man/transform.Rd
index 083006b6..e676d36c 100644
--- a/man/transform.Rd
+++ b/man/transform.Rd
@@ -6,10 +6,10 @@
 \alias{transform,flowSet-method}
 \title{Transform a flowFrame or flowSet}
 \usage{
-\S4method{transform}{flowFrame}(`_data`, translist, ...)
+\S4method{transform}{flowFrame}(x, translist, ...)
 }
 \arguments{
-\item{_data}{a flowFrame or flowSet object}
+\item{x}{a flowFrame or flowSet object}
 
 \item{translist}{a transformList object}
 
diff --git a/src/inPolygon.cpp b/src/inPolygon.cpp
index 4da7c45e..652b7fe2 100644
--- a/src/inPolygon.cpp
+++ b/src/inPolygon.cpp
@@ -19,7 +19,7 @@
   int nrd = data.nrow();
   int nrv = vertices.nrow();
   
-  /* check input argument _data */
+  /* check input argument x */
   if(nrd == 0)
   {
     std::vector<bool> res(nrd, false);