Refactor tidy_ function parameters from 'object' to 'x' for consistency and clarity; update documentation accordingly.

Author: stemangiola

R/methods.R

@@ -19,7 +19,7 @@ setClass("tidySummarizedExperiment",
 #' @importFrom generics tidy
 
 #' @importFrom lifecycle deprecate_warn
-tidy_ <- function(object) {
+tidy_ <- function(x, ...) {
 
     # DEPRECATE
     deprecate_warn(
@@ -28,20 +28,22 @@ 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