From de2074168289956c7a41114d30f700f526d9ebba Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Sat, 28 Oct 2023 18:07:41 +1100
Subject: [PATCH] drop sample argument

---
 R/methods.R | 29 +++++++++++++++++++++--------
 1 file changed, 21 insertions(+), 8 deletions(-)

diff --git a/R/methods.R b/R/methods.R
index afa7b3d4..ec4f545c 100755
--- a/R/methods.R
+++ b/R/methods.R
@@ -3927,11 +3927,17 @@ setGeneric("test_gene_rank", function(.data,
 
 	}
 
+	# DEPRECATION OF reference function
+	if (is_present(.sample) & !is.null(.sample)) {
+	  
+	  # Signal the deprecation to the user
+	  deprecate_warn("1.13.2", "tidybulk::test_gene_rank(.sample = )", details = "The argument .sample is now deprecated and not needed anymore.")
+
+	}
+	
 	# Get column names
-  	.sample = enquo(.sample)
-  	.sample =  get_sample(.data, .sample)$.sample
-  	.arrange_desc = enquo(.arrange_desc)
-  	.entrez = enquo(.entrez)
+	.arrange_desc = enquo(.arrange_desc)
+	.entrez = enquo(.entrez)
 
 	# Check if ranking is set
 	if(quo_is_missing(.arrange_desc))
@@ -3955,19 +3961,26 @@ setGeneric("test_gene_rank", function(.data,
 	# Check if missing entrez
 	if(.data |> filter(is.na(!!.entrez)) |> nrow() > 0 ){
 		warning("tidybulk says: there are .entrez that are NA. Those will be removed")
-		.data = .data |>	filter(!!.entrez |> is.na() |> not())
+		.data = .data |>	filter(is.na(!!.entrez) |> not())
 	}
 
 	# Check if missing .arrange_desc
 	if(.data |> filter(is.na(!!.arrange_desc)) |> nrow() > 0 ){
 		warning("tidybulk says: there are .arrange_desc that are NA. Those will be removed")
-		.data = .data |>	filter(!!.arrange_desc |> is.na() |> not())
+		.data = .data |>	filter(is.na(!!.arrange_desc ) |> not())
 	}
 
 	.data |>
-		pivot_transcript(!!.entrez) |>
-		arrange(desc(!!.arrange_desc)) |>
 		select(!!.entrez, !!.arrange_desc) |>
+	  distinct() |> 
+	  
+	  # Select one entrez - NEEDED?
+	  with_groups(c(!!.entrez,!!.arrange_desc ), slice, 1) |> 
+
+	  # arrange 
+	  arrange(desc(!!.arrange_desc)) |>
+	  
+	  # Format
 		deframe() |>
 		entrez_rank_to_gsea(species, gene_collections  = gene_sets ) |>