Use new BiocGenerics::transform() with new signature

DESCRIPTION

@@ -16,7 +16,7 @@ License_restricts_use: no
 LazyLoad: yes
 Imports:
     Biobase,
-    BiocGenerics,
+    BiocGenerics (>= 0.59.5),
     cytolib (>= 2.13.1),
     XML,
     ggplot2,

NAMESPACE

@@ -317,6 +317,7 @@ importFrom(Biobase,sampleNames)
 importFrom(BiocGenerics,"rownames<-")
 importFrom(BiocGenerics,duplicated)
 importFrom(BiocGenerics,rownames)
+importFrom(BiocGenerics,transform)
 importFrom(Rgraphviz,agread)
 importFrom(S4Vectors,coolcat)
 importFrom(cytolib,cytolib_LdFlags)

R/GatingSetList_Methods.R

@@ -311,11 +311,12 @@ setMethod("keyword",c("GatingSetList","character"),function(object,keyword){
 }
 
 #' @export
+#' @importFrom BiocGenerics transform
 setMethod("transform",
-    signature = signature(`_data` = "GatingSetList"),
-    definition = function(`_data`, ...)
+    signature = signature(x = "GatingSetList"),
+    definition = function(x, ...)
     {
-      res <- lapply(`_data`, function(gs)transform(gs, ...), level = 1)
+      res <- lapply(x, function(gs)transform(gs, ...), level = 1)
       GatingSetList(res)
     })
 

R/GatingSet_Methods.R

@@ -982,7 +982,7 @@ gs_keyword_set <- function(gs, keys, values){
 #' 
 #' @name transform
 #' @aliases transform,GatingSetList-method transform,GatingSet-method
-#' @param _data \code{GatingSet} or \code{GatingSetList}
+#' @param x \code{GatingSet} or \code{GatingSetList}
 #' @param translist expect a \code{transformList} object or a list of \code{transformList} objects(with names matched to sample names)
 #' @param ... other arguments passed to 'transform' method for 'ncdfFlowSet'.(e.g. 'ncdfFile')
 #' @return a \code{GatingSet} or \code{GatingSetList} object with the underling flow data transformed.
@@ -1005,12 +1005,13 @@ gs_keyword_set <- function(gs, keys, values){
 #'
 #' }
 #' @export
+#' @importFrom BiocGenerics transform
 setMethod("transform",
-    signature = signature(`_data` = "GatingSet"),
-    definition = function(`_data`, translist, ...)
+    signature = signature(x = "GatingSet"),
+    definition = function(x, translist, ...)
     {
 
-      gs <- `_data`
+      gs <- x
       # browser()
       if(missing(translist))
         stop("Missing the second argument 'translist'!")

R/cytoframe.R

@@ -588,9 +588,10 @@ setReplaceMethod("parameters",
 			return(object)
 		})
 
+#' @importFrom BiocGenerics transform
 setMethod("transform",
-          signature=signature(`_data`="cytoframe"),
-          definition=function(`_data`, translist, ...)
+          signature=signature(x="cytoframe"),
+          definition=function(x, translist, ...)
           {
             if(missing(translist))
               stop("Missing the second argument 'translist'!")
@@ -626,11 +627,11 @@ setMethod("transform",
             if(is(tList, "transformList")){
               # flowCore %on% method for flowFrame
               # Also updates keywords: "transformation", "PnRmax", "PnRmin"
-              return(tList %on% `_data`)
+              return(tList %on% x)
             }else{
               # Do the transformation at the C++ level
-              cf_transform_data(`_data`@pointer, tList)
-              return(`_data`)
+              cf_transform_data(x@pointer, tList)
+              return(x)
             }
 
           })

R/cytoset.R

@@ -553,36 +553,37 @@ setMethod("compensate", signature=signature(x="cytoset", spillover="list"),#expl
           })
 
 #' @export
+#' @importFrom BiocGenerics transform
 setMethod("transform",
-	  signature=signature(`_data`="cytoset"),
-	  definition=function(`_data`, translist,...)
+	  signature=signature(x="cytoset"),
+	  definition=function(x, translist,...)
 	  {
 		  if(missing(translist))
 			  stop("Missing the second argument 'translist'!")
 		  else if(is(translist, "transformList"))
 		  {
-			  translist <- sapply(sampleNames(`_data`), function(obj)translist, simplify = FALSE)
+			  translist <- sapply(sampleNames(x), function(obj)translist, simplify = FALSE)
 		  }
 	    if(is(translist, "list"))
 	    {
 	      tList <- lapply(translist, function(trans){
 	        if(!is(trans, "transformList"))
 	          stop("All the elements of 'translist' must be 'transformList' objects!")
 	        })
-	      sns <- sampleNames(`_data`)
+	      sns <- sampleNames(x)
 	      if(!setequal(sns, names(translist)))
 	        stop("names of 'translist' must be consistent with flow data!")
-	      for(sn in sampleNames(`_data`))
+	      for(sn in sampleNames(x))
 	      {
-	        cf <- get_cytoframe_from_cs(`_data`, sn)
+	        cf <- get_cytoframe_from_cs(x, sn)
 	        transform(cf, translist[[sn]], ...)
 	      }
       }else
 			  stop("expect the second argument as a 'transformList' object or a list of 'transformList' objects!")
 
 
 
-		  `_data`
+		  x
 	  })
 setMethod("identifier",
 		signature=signature(object="cytoset"),
@@ -1050,4 +1051,4 @@ cs_keyword_set <- function(cs, keys, values){
     stop("keys and values must be character vectors of equal length")
   for(idx in seq_along(cs))
     cf_setKeywordsSubset(cs[[idx]]@pointer, keys, as.character(values))
-}
+}