Import S4 class and export new methods

ropensci · Feb 8, 2025 · 4691dff · 4691dff
1 parent 40754c6
commit 4691dff
Show file tree

Hide file tree

Showing 3 changed files with 21 additions and 12 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -176,13 +176,17 @@ exportMethods(set_size)
 exportMethods(sets)
 exportMethods(show)
 exportMethods(subtract)
+if (requireNamespace("AnnotationDbi", quietly = TRUE)) {
+importClassesFrom(AnnotationDbi, Go3AnnDbBimap)
+S3method("tidySet", Go3AnnDbBimap)
+}
 if (requireNamespace("GSEABase", quietly = TRUE)) {
-importClassesFrom(GSEABase, GeneSetCollection)
-S3method(tidy, GeneSetCollection)
-importClassesFrom(GSEABase, GeneSet)
-S3method(tidy, GeneSet)
-importClassesFrom(GSEABase, CollectionType)
-S3method(tidy, CollectionType)
+importClassesFrom("GSEABase", GeneSetCollection)
+S3method("tidy", GeneSetCollection)
+importClassesFrom("GSEABase", GeneSet)
+S3method("tidy", GeneSet)
+importClassesFrom("GSEABase", CollectionType)
+S3method("tidy", CollectionType)
 }
 importFrom(dplyr,arrange)
 importFrom(dplyr,filter)

diff --git a/R/GeneSetCollection.R b/R/GeneSetCollection.R
@@ -1,11 +1,11 @@
 #' @include AllClasses.R AllGenerics.R
 #' @rawNamespace if (requireNamespace("GSEABase", quietly = TRUE)) {
-#' importClassesFrom(GSEABase, GeneSetCollection)
-#' S3method(tidy, GeneSetCollection)
-#' importClassesFrom(GSEABase, GeneSet)
-#' S3method(tidy, GeneSet)
-#' importClassesFrom(GSEABase, CollectionType)
-#' S3method(tidy, CollectionType)
+#' importClassesFrom("GSEABase", GeneSetCollection)
+#' S3method("tidy", GeneSetCollection)
+#' importClassesFrom("GSEABase", GeneSet)
+#' S3method("tidy", GeneSet)
+#' importClassesFrom("GSEABase", CollectionType)
+#' S3method("tidy", CollectionType)
 #' }
 NULL
 
@@ -46,6 +46,7 @@ tidy.GeneSetCollection <- function(object) {
 
 #' @describeIn tidy Converts to a tidySet given a GeneSet
 tidy.GeneSet <- function(object) {
+
     if (length(object@geneIds) == 0) {
         elements <- character(length = 1)
     } else {

diff --git a/R/tidy-set.R b/R/tidy-set.R
@@ -1,4 +1,8 @@
 #' @include AllClasses.R
+#' @rawNamespace if (requireNamespace("AnnotationDbi", quietly = TRUE)) {
+#' importClassesFrom(AnnotationDbi, Go3AnnDbBimap)
+#' S3method("tidySet", Go3AnnDbBimap)
+#' }
 NULL
 
 #' Create a TidySet object