Merge pull request #112 from tidyomics/use-tidy-generics

rely on generics tidy

Author: stemangiola

DESCRIPTION

@@ -41,7 +41,8 @@ Imports:
     fansi,
     stats,
     pkgconfig,
-    plyxp
+    plyxp,
+    generics
 Suggests:
     BiocStyle,
     testthat,

NAMESPACE

@@ -37,7 +37,6 @@ S3method(tidy,SummarizedExperiment)
 S3method(unite,SummarizedExperiment)
 S3method(unnest,tidySummarizedExperiment_nested)
 export("%>%")
-export(tidy)
 export(unnest_summarized_experiment)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,DataFrame)
@@ -81,6 +80,7 @@ importFrom(dplyr,summarise)
 importFrom(dplyr,summarize)
 importFrom(dplyr,vars)
 importFrom(ellipsis,check_dots_used)
+importFrom(generics,tidy)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,ggplot)
 importFrom(lifecycle,deprecate_warn)

R/methods.R

@@ -6,7 +6,6 @@ setClass("tidySummarizedExperiment",
 #' @rdname tidy
 #' @title tidy for `Seurat`
 #'
-#' @param object A `Seurat` object.
 #' @return A `tidyseurat` object.
 #'
 #' @examples
@@ -16,13 +15,10 @@ setClass("tidySummarizedExperiment",
 #' @references
 #' Hutchison, W.J., Keyes, T.J., The tidyomics Consortium. et al. The tidyomics ecosystem: enhancing omic data analyses. Nat Methods 21, 1166–1170 (2024). https://doi.org/10.1038/s41592-024-02299-2
 #'
-#' @export
-tidy <- function(object) {
-    UseMethod("tidy", object)
-}
+#' @importFrom generics tidy
 
 #' @importFrom lifecycle deprecate_warn
-tidy_ <- function(object) {
+tidy_ <- function(x, ...) {
 
     # DEPRECATE
     deprecate_warn(
@@ -31,20 +27,22 @@ tidy_ <- function(object) {
         details = "tidySummarizedExperiment says: tidy() is not needed anymore."
     )
 
-    object
+    x
 }
 
 #' @importFrom methods as
 #' @rdname tidy
-#' @param object A SummarizedExperiment object
+#' @param x A SummarizedExperiment object
+#' @param ... Additional arguments passed to methods
 #' @references
 #' Hutchison, W.J., Keyes, T.J., The tidyomics Consortium. et al. The tidyomics ecosystem: enhancing omic data analyses. Nat Methods 21, 1166–1170 (2024). https://doi.org/10.1038/s41592-024-02299-2
 #' @export
 tidy.SummarizedExperiment <- tidy_
 
 #' @importFrom methods as
 #' @rdname tidy
-#' @param object A SummarizedExperiment object
+#' @param x A SummarizedExperiment object
+#' @param ... Additional arguments passed to methods
 #' @references
 #' Hutchison, W.J., Keyes, T.J., The tidyomics Consortium. et al. The tidyomics ecosystem: enhancing omic data analyses. Nat Methods 21, 1166–1170 (2024). https://doi.org/10.1038/s41592-024-02299-2
 #' @export