fixed a bug on head method

NAMESPACE

@@ -15,7 +15,6 @@ S3method(summary,pathwayRes)
 export(adjust_pval)
 export(extract)
 export(from_ASICS_to_PHOENICS)
-export(head)
 export(overlap_coefficient)
 export(pathway_search)
 export(test_pathway)
@@ -37,4 +36,5 @@ importFrom(tibble,remove_rownames)
 importFrom(tibble,rownames_to_column)
 importFrom(tidyr,pivot_wider)
 importFrom(tidyr,separate)
+importFrom(utils,head)
 importFrom(utils,read.table)

R/pathwayRes-class.R

@@ -174,19 +174,12 @@ plot.MFApath <- function(x, ..., pathway_id = NULL,
 }
 
 #' @rdname pathwayRes
-#' @aliases head
 #' @aliases head.pathwayRes
-#' @examples 
-#' head(out_test)
-#' @export
-head <- function(object) {
-  UseMethod("head")
-}
-
+#' @importFrom utils head
 #' @exportS3Method
-head.pathwayRes <- function(object){
+head.pathwayRes <- function(x, ...){
   cat("Pathways: \n")
-  names(object)
+  names(x)
 }
 
 #' @rdname pathwayRes

man/pathwayRes.Rd

@@ -5,7 +5,6 @@
 \alias{summary.pathwayRes}
 \alias{print.pathwayRes}
 \alias{plot.pathwayRes}
-\alias{head}
 \alias{head.pathwayRes}
 \alias{extract}
 \alias{extract.pathwayRes}
@@ -25,7 +24,7 @@
   habillage = "none"
 )
 
-head(object)
+\method{head}{pathwayRes}(x, ...)
 
 extract(object, pathway_id)
 
@@ -90,7 +89,6 @@ plot(out_test2, pathway_id = "mmu00562", plot = "eig")
 plot(out_test2, pathway_id = "mmu00562", plot = "var")
 plot(out_test2, pathway_id = "mmu00562", plot = "ind")
 plot(out_test2, pathway_id = "mmu00562", plot = "group")
-head(out_test)
 extract(out_test, "mmu00562")
 adj_pval <- adjust_pval(out_test)
 }