Remove CTSSclusteringMethod and stop recording clustering method name.

Storing this information in metadata slots was very fragile, complicated the code, and caused bugs.

Author: Charles Plessy

NAMESPACE

@@ -13,7 +13,6 @@ export("inputFilesType<-")
 export("sampleLabels<-")
 export(CAGEexp)
 export(CTSS)
-export(CTSSclusteringMethod)
 export(CTSScoordinatesGR)
 export(CTSScumulativesCC)
 export(CTSScumulativesTagClusters)

NEWS.md

@@ -1,5 +1,10 @@
 # Upcoming changes in version 2.11.3
 
+BACKWARDS-INCOMPATIBLE CHANGES
+
+-   Remove `CTSSclusteringMethod()` function and stop recording clustering
+    method name.
+
 NEW FEATURES
 
 -   New `resetCAGEexp()` function.
@@ -39,8 +44,7 @@ BUG FIXES
 
 # Changes in version 2.8.0 (25/10/2023)
 
-BACKWARDS-INCOMPATIBLE CHANGES
-
+ 
 -   The `CTSStagCountDA` function is removed.
 -   The _dominant peak_ in `TagClusters` objects is now a `GRanges` object like
     in `ConsensusClusters`.

R/ClusteringMethods.R

@@ -79,7 +79,7 @@
 #' 
 #' @author Vanja Haberle
 #' 
-#' @seealso [`tagClustersGR`], [`aggregateTagClusters`] and [`CTSSclusteringMethod`].
+#' @seealso [`aggregateTagClusters`]
 #' 
 #' @family CAGEr object modifiers
 #' @family CAGEr clusters functions
@@ -150,7 +150,6 @@ setMethod( "clusterCTSS", "CAGEexp"
     stop("Deprecated method.  See ", dQuote("CustomConsensusClusters()"), " instead.")
   }
 
-  CTSSclusteringMethod(ctss.cluster.list) <- method
   seqlevels(ctss.cluster.list) <- seqlevels(CTSStagCountSE(object))
   seqinfo(ctss.cluster.list)   <- seqinfo(CTSStagCountSE(object))
   # Changing the sequence levels may change the sort order.  Re-sort

R/GetMethods.R

@@ -384,40 +384,6 @@ setMethod( "CTSSnormalizedTpmGR", "CAGEexp", function (object, samples) {
   gr
 })
 
-#' @name CTSSclusteringMethod
-#' 
-#' @title Get /set CTSS clustering method
-#' 
-#' @description Returns or sets the name of the method that was used make tag
-#' clusters from the CTSSs of a \code{\link{CAGEr}} object.
-#' 
-#' @param object A CAGEr object.
-#' 
-#' @seealso \code{\link{clusterCTSS}}
-#' @family CAGEr accessor methods
-#' @family CAGEr clusters functions
-#' 
-#' @author Vanja Haberle
-#' @author Charles Plessy
-#' 
-#' @examples 
-#' CTSSclusteringMethod(exampleCAGEexp)
-#' 
-#' @export CTSSclusteringMethod
-
-setGeneric("CTSSclusteringMethod", function(object) standardGeneric("CTSSclusteringMethod"))
-
-#' @rdname CTSSclusteringMethod
-
-setMethod("CTSSclusteringMethod", "GRangesList", function (object)
-	metadata(object)$clusteringMethod)
-
-#' @rdname CTSSclusteringMethod
-
-setMethod("CTSSclusteringMethod", "CAGEexp", function (object)
-  CTSSclusteringMethod(metadata(object)$tagClusters))
-
-
 #' @name tagClustersGR
 #' @rdname tagClusters
 #' 
@@ -440,14 +406,12 @@ setMethod("CTSSclusteringMethod", "CAGEexp", function (object)
 #' start coordinate of the cluster.  Used only when
 #' `returnInterquantileWidth = TRUE`, otherwise ignored.
 #' 
-#' @return Returns a `GRangesList` or a `GRanges` object with genomic coordinates,
+#' @return Returns a `GRangesList` or a `TagClusters` object with genomic coordinates,
 #' position of dominant TSS, total CAGE signal and additional information for
 #' all TCs from specified CAGE dataset (sample).  If
 #' `returnInterquantileWidth = TRUE`, interquantile width for each TC is also
 #' calculated using provided quantile positions.  The [`S4Vectors::metadata`]
-#' slot of the object contains a copy of the `CAGEexp` object's _column data_,
-#' as well as information on the clustering method in a `clusteringMethod`
-#' element.
+#' slot of the object contains a copy of the `CAGEexp` object's _column data_.
 #' 
 #' @author Vanja Haberle
 #' @author Charles Plessy
@@ -460,7 +424,6 @@ setMethod("CTSSclusteringMethod", "CAGEexp", function (object)
 #' tagClustersGR( exampleCAGEexp, "Zf.high", TRUE, 0.1, 0.9 )
 #' tagClustersGR( exampleCAGEexp, 1
 #'              , returnInterquantileWidth = TRUE, qLow = 0.1, qUp = 0.9 )
-#' tagClustersGR( exampleCAGEexp )$clusteringMethod
 #' tagClustersGR( exampleCAGEexp )@metadata$colData
 #' 
 #' @export
@@ -475,7 +438,6 @@ setGeneric( "tagClustersGR"
                                   , returnInterquantileWidth = returnInterquantileWidth
                                   , qLow = qLow, qUp = qUp))
     names(tc.list) <- sampleLabels(object)
-    metadata(tc.list)$clusteringMethod <- CTSSclusteringMethod(object)
     metadata(tc.list)$colData <- colData(object)
     return(tc.list)
   }

R/SetMethods.R

@@ -159,33 +159,6 @@ setMethod("filteredCTSSidx<-", "CAGEexp", function (object, value) {
   if (validObject(object)) object
 })
 
-
-#' @name CTSSclusteringMethod<-
-#' 
-#' @rdname CTSSclusteringMethod
-#' 
-#' @param value character
-
-setGeneric( "CTSSclusteringMethod<-"
-          , function(object, value) standardGeneric("CTSSclusteringMethod<-"))
-
-#' @rdname CTSSclusteringMethod
-
-setMethod("CTSSclusteringMethod<-", "GRangesList", function (object, value) {
-  metadata(object)$clusteringMethod <- value
-  if (validObject(object)) object
-})
-
-#' @rdname CTSSclusteringMethod
-
-setMethod("CTSSclusteringMethod<-", "CAGEexp", function (object, value) {
-  CTSSclusteringMethod(metadata(object)$tagClusters) <- value
-  # extrat directly TCs from metadata slot because tagClustersGR does more that
-  # is not needed here.
-  if (validObject(object)) object
-})
-
-
 #' @name  CTSScumulativesTagClusters<-
 #' 
 #' @rdname CTSScumulativesTagClusters