use drops() for bookkeeping instead of metadata() when assays are rem…

…oved

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(.DollarNames,MultiAssayExperiment)
+export("drops<-")
 export("experiments<-")
 export("sampleMap<-")
 export(DataFrame)
@@ -9,6 +10,7 @@ export(MatchedAssayExperiment)
 export(MultiAssayExperiment)
 export(MultiAssayExperimentToMAF)
 export(anyReplicated)
+export(drops)
 export(experiments)
 export(exportClass)
 export(getWithColData)
@@ -47,7 +49,6 @@ exportMethods("[[<-")
 exportMethods("colData<-")
 exportMethods("colnames<-")
 exportMethods("experiments<-")
-exportMethods("metadata<-")
 exportMethods("names<-")
 exportMethods("sampleMap<-")
 exportMethods(anyReplicated)
@@ -58,13 +59,13 @@ exportMethods(colData)
 exportMethods(colnames)
 exportMethods(complete.cases)
 exportMethods(dimnames)
+exportMethods(drops)
 exportMethods(experiments)
 exportMethods(exportClass)
 exportMethods(hasRowRanges)
 exportMethods(isEmpty)
 exportMethods(length)
 exportMethods(mergeReplicates)
-exportMethods(metadata)
 exportMethods(names)
 exportMethods(replicated)
 exportMethods(replicates)

R/MultiAssayExperiment-class.R

@@ -573,12 +573,6 @@ setMethod("colData", "MultiAssayExperiment", function(x, ...) {
     getElement(x, "colData")
 })
 
-#' @exportMethod metadata
-#' @rdname MultiAssayExperiment-methods
-setMethod("metadata", "MultiAssayExperiment", function(x)
-    c(getElement(x, "metadata"), drops = getElement(x, "drops"))
-)
-
 ### - - - - - - - - - - - - - - - - - - - - - - - -
 ### Getters
 ###
@@ -595,6 +589,15 @@ setMethod("names", "MultiAssayExperiment", function(x)
     names(experiments(x))
 )
 
+#' @export
+setGeneric("drops", function(x) standardGeneric("drops"))
+
+#' @exportMethod drops
+#' @describeIn MultiAssayExperiment Get information about dropped experiments
+setMethod("drops", "MultiAssayExperiment", function(x) {
+    getElement(x, "drops")
+})
+
 ### - - - - - - - - - - - - - - - - - - - - - - - -
 ### Replacers
 ###
@@ -636,16 +639,18 @@ setReplaceMethod("sampleMap", c("MultiAssayExperiment", "ANY"),
 setGeneric("experiments<-", function(object, value)
     standardGeneric("experiments<-"))
 
+#' @export
 setGeneric("drops<-", function(x, ..., value) standardGeneric("drops<-"))
 
 #' @exportMethod experiments<-
 #' @rdname MultiAssayExperiment-methods
 setReplaceMethod("experiments", c("MultiAssayExperiment", "ExperimentList"),
     function(object, value) {
         if (!any(names(object) %in% names(value)) && !isEmpty(object)) {
+            if (isEmpty(drops(x)))
+                warning("'experiments' dropped; see 'drops()'", call. = FALSE)
             drops(object) <-
                 list(experiments = setdiff(names(object), names(value)))
-            warning("'experiments' dropped; see 'metadata'", call. = FALSE)
         }
         o_cnames <- colnames(object)
         v_cnames <- colnames(value)
@@ -732,13 +737,6 @@ setReplaceMethod("colData", c("MultiAssayExperiment", "ANY"),
     }
 )
 
-#' @exportMethod metadata<-
-#' @rdname MultiAssayExperiment-methods
-setReplaceMethod("metadata", c("MultiAssayExperiment", "ANY"),
-    function(x, ..., value) {
-        slot(x, "metadata") <- value
-        return(x)
-})
 
 setReplaceMethod("drops", c("MultiAssayExperiment", "ANY"),
     function(x, ..., value) {

R/subsetBy-methods.R

@@ -333,8 +333,9 @@ setMethod("subsetByAssay", c("MultiAssayExperiment", "ANY"), function(x, y) {
     subexp <- experiments(x)[y]
     dropnames <- setdiff(names(experiments(x)), names(subexp))
     if (length(dropnames)) {
+        if (isEmpty(drops(x)))
+            warning("'experiments' dropped; see 'drops()'", call. = FALSE)
         drops(x) <- list(experiments = dropnames)
-        warning("'experiments' dropped; see 'metadata'", call. = FALSE)
     }
     experiments(x) <- subexp
     return(x)