deprecate default method

R/methods.R

@@ -2676,14 +2676,15 @@ setMethod("ensembl_to_symbol", "tidybulk", .ensembl_to_symbol)
 #'
 #'  tidybulk::se_mini |>
 #'  identify_abundant() |>
-#' 	test_differential_abundance( ~ condition )
+#' 	test_differential_abundance( ~ condition, method = "edgeR_quasi_likelihood" )
 #'
 #' 	# The function `test_differential_abundance` operates with contrasts too
 #'
 #'  tidybulk::se_mini |>
 #'  identify_abundant(factor_of_interest = condition) |>
 #'  test_differential_abundance(
 #' 	    ~ 0 + condition,
+#' 	    method = "edgeR_quasi_likelihood",
 #' 	    contrasts = c( "conditionTRUE - conditionFALSE")
 #'  )
 #'
@@ -2742,7 +2743,7 @@ setGeneric("test_differential_abundance", function(.data,
 																									 .transcript = NULL,
 																									 .abundance = NULL,
 																									 contrasts = NULL,
-																									 method = "edgeR_quasi_likelihood",
+																									 method = NULL,
 																									 test_above_log2_fold_change = NULL,
 																									 scaling_method = "TMM",
 																									 omit_contrast_in_colnames = FALSE,
@@ -2765,7 +2766,7 @@ setGeneric("test_differential_abundance", function(.data,
 																					.transcript = NULL,
 																					.abundance = NULL,
 																					contrasts = NULL,
-																					method = "edgeR_quasi_likelihood",
+																					method = NULL,
 																					test_above_log2_fold_change = NULL,
 																					scaling_method = "TMM",
 																					omit_contrast_in_colnames = FALSE,
@@ -2793,11 +2794,23 @@ setGeneric("test_differential_abundance", function(.data,
 	.transcript = col_names$.transcript
 	.abundance = col_names$.abundance
 
+
+
+
+	# DEPRECATION OF method = "edgeR_quasi_likelihood"
+	if (is.null(method)) {
+
+	  # Signal the deprecation to the user
+	  warning("In Jannuary 2024 the `method` argument will need to be specified and must NOT be empty. Until then method = NULL will be defaulted to \"edgeR_quasi_likelihood\" as for consistency with old version.")
+
+	  method = "edgeR_quasi_likelihood"
+	}
+
 	# DEPRECATION OF significance_threshold
 	if (is_present(significance_threshold) & !is.null(significance_threshold)) {
 
 		# Signal the deprecation to the user
-		deprecate_warn("1.1.7", "tidybulk::test_differential_abundance(significance_threshold = )", details = "The argument significance_threshold is now deprecated, tigether with the column significance.")
+		deprecate_warn("1.1.7", "tidybulk::test_differential_abundance(significance_threshold = )", details = "The argument significance_threshold is now deprecated, together with the column significance.")
 
 	}
 

tests/testthat/test-bulk_methods.R

@@ -807,6 +807,7 @@ test_that("DESeq2 differential trancript abundance - no object",{
 			.sample = a,
 			.transcript = b,
 			.abundance = c,
+			method = "edgeR_quasi_likelihood",
 			contrasts = "conditionTRUE - conditionFALSE",
 			action="only"
 		)

tests/testthat/test-bulk_methods_SummarizedExperiment.R

@@ -284,7 +284,9 @@ test_that("differential trancript abundance - SummarizedExperiment",{
   res =		test_differential_abundance(
     se_mini |>
       identify_abundant(factor_of_interest = condition),
-    ~ condition
+    ~ condition,
+    method = "edgeR_quasi_likelihood"
+
   )
 
   w = match(  c("CLEC7A" , "FAM198B", "FCN1"  ,  "HK3"   ), rownames(res) )
@@ -293,7 +295,8 @@ test_that("differential trancript abundance - SummarizedExperiment",{
   res_tibble =		test_differential_abundance(
     input_df |> identify_abundant(a, b, c, factor_of_interest = condition),
     ~ condition	,
-    a, b, c
+    a, b, c,
+    method = "edgeR_quasi_likelihood"
   )
 
   expect_equal(