Fix issue #120 and push to Bioc

charles-plessy · Aug 2, 2024 · fa1432a · fa1432a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: CAGEr
 Title: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
-Version: 2.11.3
-Date: 2024-05-24
+Version: 2.11.4
+Date: 2024-08-02
 Authors@R:
   c( person("Vanja",   "Haberle",   email = "[email protected]",       role = "aut"),
      person("Charles", "Plessy",    email = "[email protected]",        role = "cre"),

diff --git a/NAMESPACE b/NAMESPACE
@@ -40,6 +40,7 @@ export(distclu)
 export(exportToTrack)
 export(expressionClasses)
 export(filterLowExpCTSS)
+export(filteredCTSSidx)
 export(findStrandInvaders)
 export(flagByUpstreamSequences)
 export(flagLowExpCTSS)

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# Upcoming changes in version 2.11.4
+# Changes in version 2.11.4
 
 BACKWARDS-INCOMPATIBLE CHANGES
 
@@ -8,6 +8,11 @@ NEW FEATURES
 
 -   Support the use of `TxDB` objects for annotating clusters.
 
+BUG FIXES
+
+-   Fix issue #120 introduced in 2.11.3, where clustering functions would
+    fail if `filterLowExpCTSS` was not run before.
+
 # Changes in version 2.11.3
 
 BACKWARDS-INCOMPATIBLE CHANGES

diff --git a/R/CAGEr.R b/R/CAGEr.R
@@ -182,6 +182,8 @@ setMethod("validSamples", "CAGEr", function (object, x){
 #' 
 #' @export
 #' 
+#' @family CAGEr filter functions
+#' 
 #' @examples
 #' flagLowExpCTSS(exampleCAGEexp, threshold = 100, nrPassThreshold = 2)
 

diff --git a/R/GetMethods.R b/R/GetMethods.R
@@ -454,13 +454,32 @@ setMethod( "tagClustersGR", "CAGEexp"
   .TagClusters(tc)
 })
 
-#' @name filteredCTSSidx
-#' @noRd
+#' The `filteredCTSSidx()` function is in _CAGEr_ functions to retrieve the
+#' result of the `flagLowExpCTSS()` function in a safe way.
+#' 
+#' @returns Returns the value of `filteredCTSSidx` in the row ranges of the
+#' tag count matrix experiment of the `CAGEexp` object, or `Rle(TRUE)` if it
+#' was `NULL`
+#' 
+#' @param object A [`CAGEexp`] object
+#' 
+#' @export
+#' 
+#' @examples
+#' 
+#' filteredCTSSidx(exampleCAGEexp)
+#' 
+#' @family CAGEr filter functions
+#' @family CAGEr accessor methods
 
 setGeneric("filteredCTSSidx", function(object) standardGeneric("filteredCTSSidx"))
 
+#' @rdname filteredCTSSidx
+
 setMethod("filteredCTSSidx", "CAGEexp", function (object){
-  rowData(CTSStagCountSE(object))$filteredCTSSidx
+  res <- rowData(CTSStagCountSE(object))$filteredCTSSidx
+  if (is.null(res)) return(Rle(TRUE))
+  res
 })
 
 

diff --git a/man/CTSScoordinates.Rd b/man/CTSScoordinates.Rd
diff --git a/man/CTSScumulativesTagClusters.Rd b/man/CTSScumulativesTagClusters.Rd
diff --git a/man/CTSSnormalizedTpm.Rd b/man/CTSSnormalizedTpm.Rd
diff --git a/man/CTSStagCount.Rd b/man/CTSStagCount.Rd
diff --git a/man/GeneExpDESeq2.Rd b/man/GeneExpDESeq2.Rd
diff --git a/man/GeneExpSE.Rd b/man/GeneExpSE.Rd
diff --git a/man/consensusClusters.Rd b/man/consensusClusters.Rd
diff --git a/man/expressionClasses.Rd b/man/expressionClasses.Rd
diff --git a/man/filteredCTSSidx.Rd b/man/filteredCTSSidx.Rd
diff --git a/man/flagByUpstreamSequences.Rd b/man/flagByUpstreamSequences.Rd
diff --git a/man/flagLowExpCTSS.Rd b/man/flagLowExpCTSS.Rd
diff --git a/man/genomeName.Rd b/man/genomeName.Rd
diff --git a/man/inputFiles.Rd b/man/inputFiles.Rd
diff --git a/man/inputFilesType.Rd b/man/inputFilesType.Rd
diff --git a/man/librarySizes.Rd b/man/librarySizes.Rd
diff --git a/man/sampleLabels.Rd b/man/sampleLabels.Rd
diff --git a/man/seqNameTotalsSE.Rd b/man/seqNameTotalsSE.Rd
diff --git a/man/tagClusters.Rd b/man/tagClusters.Rd