diff --git a/NAMESPACE b/NAMESPACE
index b987f70..96d7863 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -13,7 +13,6 @@ export("inputFilesType<-")
 export("sampleLabels<-")
 export(CAGEexp)
 export(CTSS)
-export(CTSSclusteringMethod)
 export(CTSScoordinatesGR)
 export(CTSScumulativesCC)
 export(CTSScumulativesTagClusters)
diff --git a/NEWS.md b/NEWS.md
index e2fa4ab..6a3d009 100644
--- a/NEWS.md
+++ b/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`.
diff --git a/R/ClusteringMethods.R b/R/ClusteringMethods.R
index 6d80281..e0ff140 100644
--- a/R/ClusteringMethods.R
+++ b/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
diff --git a/R/GetMethods.R b/R/GetMethods.R
index a9eb642..8d7a70a 100644
--- a/R/GetMethods.R
+++ b/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)
   }
diff --git a/R/SetMethods.R b/R/SetMethods.R
index 6972e3a..378a0dd 100644
--- a/R/SetMethods.R
+++ b/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
diff --git a/data/exampleCAGEexp.RData b/data/exampleCAGEexp.RData
index 9e1763b..8494c63 100644
Binary files a/data/exampleCAGEexp.RData and b/data/exampleCAGEexp.RData differ
diff --git a/man/CTSSclusteringMethod.Rd b/man/CTSSclusteringMethod.Rd
deleted file mode 100644
index ec99a98..0000000
--- a/man/CTSSclusteringMethod.Rd
+++ /dev/null
@@ -1,75 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/GetMethods.R, R/SetMethods.R
-\name{CTSSclusteringMethod}
-\alias{CTSSclusteringMethod}
-\alias{CTSSclusteringMethod,GRangesList-method}
-\alias{CTSSclusteringMethod,CAGEexp-method}
-\alias{CTSSclusteringMethod<-}
-\alias{CTSSclusteringMethod<-,GRangesList-method}
-\alias{CTSSclusteringMethod<-,CAGEexp-method}
-\title{Get /set CTSS clustering method}
-\usage{
-CTSSclusteringMethod(object)
-
-\S4method{CTSSclusteringMethod}{GRangesList}(object)
-
-\S4method{CTSSclusteringMethod}{CAGEexp}(object)
-
-CTSSclusteringMethod(object) <- value
-
-\S4method{CTSSclusteringMethod}{GRangesList}(object) <- value
-
-\S4method{CTSSclusteringMethod}{CAGEexp}(object) <- value
-}
-\arguments{
-\item{object}{A CAGEr object.}
-
-\item{value}{character}
-}
-\description{
-Returns or sets the name of the method that was used make tag
-clusters from the CTSSs of a \code{\link{CAGEr}} object.
-}
-\examples{
-CTSSclusteringMethod(exampleCAGEexp)
-
-}
-\seealso{
-\code{\link{clusterCTSS}}
-
-Other CAGEr accessor methods: 
-\code{\link{CTSScoordinatesGR}()},
-\code{\link{CTSScumulativesTagClusters}()},
-\code{\link{CTSSnormalizedTpmDF}()},
-\code{\link{CTSStagCountDF}()},
-\code{\link{GeneExpDESeq2}()},
-\code{\link{GeneExpSE}()},
-\code{\link{consensusClustersGR}()},
-\code{\link{expressionClasses}()},
-\code{\link{genomeName}()},
-\code{\link{inputFiles}()},
-\code{\link{inputFilesType}()},
-\code{\link{librarySizes}()},
-\code{\link{sampleLabels}()},
-\code{\link{seqNameTotalsSE}()},
-\code{\link{tagClustersGR}()}
-
-Other CAGEr clusters functions: 
-\code{\link{CTSScumulativesTagClusters}()},
-\code{\link{CustomConsensusClusters}()},
-\code{\link{aggregateTagClusters}()},
-\code{\link{clusterCTSS}()},
-\code{\link{consensusClustersDESeq2}()},
-\code{\link{consensusClustersGR}()},
-\code{\link{cumulativeCTSSdistribution}()},
-\code{\link{plotInterquantileWidth}()},
-\code{\link{quantilePositions}()},
-\code{\link{tagClustersGR}()}
-}
-\author{
-Vanja Haberle
-
-Charles Plessy
-}
-\concept{CAGEr accessor methods}
-\concept{CAGEr clusters functions}
diff --git a/man/CTSScoordinates.Rd b/man/CTSScoordinates.Rd
index eafab1f..f6a24b9 100644
--- a/man/CTSScoordinates.Rd
+++ b/man/CTSScoordinates.Rd
@@ -47,7 +47,6 @@ CTSScoordinatesGR(exampleCAGEexp)
 \code{\link{clusterCTSS}}
 
 Other CAGEr accessor methods: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CTSSnormalizedTpmDF}()},
 \code{\link{CTSStagCountDF}()},
diff --git a/man/CTSScumulativesTagClusters.Rd b/man/CTSScumulativesTagClusters.Rd
index 6daa6a1..b5e36e2 100644
--- a/man/CTSScumulativesTagClusters.Rd
+++ b/man/CTSScumulativesTagClusters.Rd
@@ -36,7 +36,6 @@ Accessor function.
 }
 \seealso{
 Other CAGEr clusters functions: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CustomConsensusClusters}()},
 \code{\link{aggregateTagClusters}()},
 \code{\link{clusterCTSS}()},
@@ -48,7 +47,6 @@ Other CAGEr clusters functions:
 \code{\link{tagClustersGR}()}
 
 Other CAGEr accessor methods: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScoordinatesGR}()},
 \code{\link{CTSSnormalizedTpmDF}()},
 \code{\link{CTSStagCountDF}()},
diff --git a/man/CTSSnormalizedTpm.Rd b/man/CTSSnormalizedTpm.Rd
index aa68310..6da6318 100644
--- a/man/CTSSnormalizedTpm.Rd
+++ b/man/CTSSnormalizedTpm.Rd
@@ -39,7 +39,6 @@ exampleCAGEexp |> CTSSnormalizedTpmGR("all")
 \code{\link{normalizeTagCount}}
 
 Other CAGEr accessor methods: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScoordinatesGR}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CTSStagCountDF}()},
diff --git a/man/CTSStagCount.Rd b/man/CTSStagCount.Rd
index 3088d53..8d16071 100644
--- a/man/CTSStagCount.Rd
+++ b/man/CTSStagCount.Rd
@@ -56,7 +56,6 @@ CTSStagCountSE(exampleCAGEexp)
 \code{\link[=getCTSS]{getCTSS()}}
 
 Other CAGEr accessor methods: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScoordinatesGR}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CTSSnormalizedTpmDF}()},
diff --git a/man/CustomConsensusClusters.Rd b/man/CustomConsensusClusters.Rd
index 6749d51..52fb70d 100644
--- a/man/CustomConsensusClusters.Rd
+++ b/man/CustomConsensusClusters.Rd
@@ -71,7 +71,6 @@ Other CAGEr object modifiers:
 \code{\link{summariseChrExpr}()}
 
 Other CAGEr clusters functions: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{aggregateTagClusters}()},
 \code{\link{clusterCTSS}()},
diff --git a/man/GeneExpDESeq2.Rd b/man/GeneExpDESeq2.Rd
index a73cc3d..a31e2fd 100644
--- a/man/GeneExpDESeq2.Rd
+++ b/man/GeneExpDESeq2.Rd
@@ -33,7 +33,6 @@ Other CAGEr gene expression analysis functions:
 \code{\link{ranges2genes}()}
 
 Other CAGEr accessor methods: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScoordinatesGR}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CTSSnormalizedTpmDF}()},
diff --git a/man/GeneExpSE.Rd b/man/GeneExpSE.Rd
index 0ac79fc..5445e1b 100644
--- a/man/GeneExpSE.Rd
+++ b/man/GeneExpSE.Rd
@@ -23,7 +23,6 @@ GeneExpSE(exampleCAGEexp)
 }
 \seealso{
 Other CAGEr accessor methods: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScoordinatesGR}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CTSSnormalizedTpmDF}()},
diff --git a/man/aggregateTagClusters.Rd b/man/aggregateTagClusters.Rd
index 5faf0ee..b4c7cb9 100644
--- a/man/aggregateTagClusters.Rd
+++ b/man/aggregateTagClusters.Rd
@@ -116,7 +116,6 @@ Other CAGEr object modifiers:
 \code{\link{summariseChrExpr}()}
 
 Other CAGEr clusters functions: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CustomConsensusClusters}()},
 \code{\link{clusterCTSS}()},
diff --git a/man/clusterCTSS.Rd b/man/clusterCTSS.Rd
index e7ecbd6..f086bb7 100644
--- a/man/clusterCTSS.Rd
+++ b/man/clusterCTSS.Rd
@@ -133,7 +133,7 @@ mammalian genomes, \emph{Genome Research} \strong{18}(1):1-12,
 (\href{http://www.cbrc.jp/paraclu/}{http://www.cbrc.jp/paraclu/}).
 }
 \seealso{
-\code{\link{tagClustersGR}}, \code{\link{aggregateTagClusters}} and \code{\link{CTSSclusteringMethod}}.
+\code{\link{aggregateTagClusters}}
 
 Other CAGEr object modifiers: 
 \code{\link{CTSStoGenes}()},
@@ -149,7 +149,6 @@ Other CAGEr object modifiers:
 \code{\link{summariseChrExpr}()}
 
 Other CAGEr clusters functions: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CustomConsensusClusters}()},
 \code{\link{aggregateTagClusters}()},
diff --git a/man/consensusClusters.Rd b/man/consensusClusters.Rd
index 1961eaa..77516e5 100644
--- a/man/consensusClusters.Rd
+++ b/man/consensusClusters.Rd
@@ -77,7 +77,6 @@ consensusClustersGR( exampleCAGEexp, sample = 2
 \code{\link[=consensusClusters<-]{consensusClusters<-()}}
 
 Other CAGEr accessor methods: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScoordinatesGR}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CTSSnormalizedTpmDF}()},
@@ -94,7 +93,6 @@ Other CAGEr accessor methods:
 \code{\link{tagClustersGR}()}
 
 Other CAGEr clusters functions: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CustomConsensusClusters}()},
 \code{\link{aggregateTagClusters}()},
diff --git a/man/consensusClustersDESeq2.Rd b/man/consensusClustersDESeq2.Rd
index edbda42..71038fc 100644
--- a/man/consensusClustersDESeq2.Rd
+++ b/man/consensusClustersDESeq2.Rd
@@ -29,7 +29,6 @@ consensusClustersDESeq2(exampleCAGEexp, ~group)
 \code{DESeqDataSet} in the \code{DESeq2} package.
 
 Other CAGEr clusters functions: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CustomConsensusClusters}()},
 \code{\link{aggregateTagClusters}()},
diff --git a/man/cumulativeCTSSdistribution.Rd b/man/cumulativeCTSSdistribution.Rd
index cc92dba..71481de 100644
--- a/man/cumulativeCTSSdistribution.Rd
+++ b/man/cumulativeCTSSdistribution.Rd
@@ -62,7 +62,6 @@ Other CAGEr object modifiers:
 \code{\link{summariseChrExpr}()}
 
 Other CAGEr clusters functions: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CustomConsensusClusters}()},
 \code{\link{aggregateTagClusters}()},
diff --git a/man/expressionClasses.Rd b/man/expressionClasses.Rd
index 8f6c5c4..ef0aaf4 100644
--- a/man/expressionClasses.Rd
+++ b/man/expressionClasses.Rd
@@ -35,7 +35,6 @@ Other CAGEr expression clustering functions:
 \code{\link{plotExpressionProfiles}()}
 
 Other CAGEr accessor methods: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScoordinatesGR}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CTSSnormalizedTpmDF}()},
diff --git a/man/genomeName.Rd b/man/genomeName.Rd
index 92d6a8e..cbce7fd 100644
--- a/man/genomeName.Rd
+++ b/man/genomeName.Rd
@@ -44,7 +44,6 @@ genomeName(exampleCAGEexp)
 }
 \seealso{
 Other CAGEr accessor methods: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScoordinatesGR}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CTSSnormalizedTpmDF}()},
diff --git a/man/inputFiles.Rd b/man/inputFiles.Rd
index de57d09..1d3bb88 100644
--- a/man/inputFiles.Rd
+++ b/man/inputFiles.Rd
@@ -33,7 +33,6 @@ inputFiles(exampleCAGEexp)
 }
 \seealso{
 Other CAGEr accessor methods: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScoordinatesGR}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CTSSnormalizedTpmDF}()},
diff --git a/man/inputFilesType.Rd b/man/inputFilesType.Rd
index f56113f..acc4494 100644
--- a/man/inputFilesType.Rd
+++ b/man/inputFilesType.Rd
@@ -67,7 +67,6 @@ inputFilesType(exampleCAGEexp)
 \code{\link{getCTSS}}
 
 Other CAGEr accessor methods: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScoordinatesGR}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CTSSnormalizedTpmDF}()},
diff --git a/man/librarySizes.Rd b/man/librarySizes.Rd
index 74fd2e4..6a7711a 100644
--- a/man/librarySizes.Rd
+++ b/man/librarySizes.Rd
@@ -33,7 +33,6 @@ librarySizes(exampleCAGEexp)
 \code{\link{getCTSS}}
 
 Other CAGEr accessor methods: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScoordinatesGR}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CTSSnormalizedTpmDF}()},
diff --git a/man/plotInterquantileWidth.Rd b/man/plotInterquantileWidth.Rd
index ace83a0..27fb37c 100644
--- a/man/plotInterquantileWidth.Rd
+++ b/man/plotInterquantileWidth.Rd
@@ -71,7 +71,6 @@ Other CAGEr plot functions:
 \code{\link{plotReverseCumulatives}()}
 
 Other CAGEr clusters functions: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CustomConsensusClusters}()},
 \code{\link{aggregateTagClusters}()},
diff --git a/man/quantilePositions.Rd b/man/quantilePositions.Rd
index 67ad354..71565f7 100644
--- a/man/quantilePositions.Rd
+++ b/man/quantilePositions.Rd
@@ -80,7 +80,6 @@ Other CAGEr object modifiers:
 \code{\link{summariseChrExpr}()}
 
 Other CAGEr clusters functions: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CustomConsensusClusters}()},
 \code{\link{aggregateTagClusters}()},
diff --git a/man/sampleLabels.Rd b/man/sampleLabels.Rd
index 146a50d..5b35997 100644
--- a/man/sampleLabels.Rd
+++ b/man/sampleLabels.Rd
@@ -70,7 +70,6 @@ sampleList(exampleCAGEexp)
 \code{\link{setColors}}
 
 Other CAGEr accessor methods: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScoordinatesGR}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CTSSnormalizedTpmDF}()},
diff --git a/man/seqNameTotalsSE.Rd b/man/seqNameTotalsSE.Rd
index cc13c44..b0eb9de 100644
--- a/man/seqNameTotalsSE.Rd
+++ b/man/seqNameTotalsSE.Rd
@@ -31,7 +31,6 @@ seqNameTotalsSE(exampleCAGEexp)
 summariseChrExpr
 
 Other CAGEr accessor methods: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScoordinatesGR}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CTSSnormalizedTpmDF}()},
diff --git a/man/tagClusters.Rd b/man/tagClusters.Rd
index 393a7ab..e0221a5 100644
--- a/man/tagClusters.Rd
+++ b/man/tagClusters.Rd
@@ -48,14 +48,12 @@ start coordinate of the cluster.  Used only when
 \item{value}{A \code{\link{TagClusters}} object.}
 }
 \value{
-Returns a \code{GRangesList} or a \code{GRanges} object with genomic coordinates,
+Returns a \code{GRangesList} or a \code{TagClusters} object with genomic coordinates,
 position of dominant TSS, total CAGE signal and additional information for
 all TCs from specified CAGE dataset (sample).  If
 \code{returnInterquantileWidth = TRUE}, interquantile width for each TC is also
 calculated using provided quantile positions.  The \code{\link[S4Vectors:Annotated-class]{S4Vectors::metadata}}
-slot of the object contains a copy of the \code{CAGEexp} object's \emph{column data},
-as well as information on the clustering method in a \code{clusteringMethod}
-element.
+slot of the object contains a copy of the \code{CAGEexp} object's \emph{column data}.
 }
 \description{
 Extracts tag clusters (TCs) produced by \code{\link{clusterCTSS}} function
@@ -65,13 +63,11 @@ for a specified CAGE experiment from a \code{\link{CAGEexp}} 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
 
 }
 \seealso{
 Other CAGEr accessor methods: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScoordinatesGR}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CTSSnormalizedTpmDF}()},
@@ -88,7 +84,6 @@ Other CAGEr accessor methods:
 \code{\link{seqNameTotalsSE}()}
 
 Other CAGEr clusters functions: 
-\code{\link{CTSSclusteringMethod}()},
 \code{\link{CTSScumulativesTagClusters}()},
 \code{\link{CustomConsensusClusters}()},
 \code{\link{aggregateTagClusters}()},