retire unused argument

ATpoint · Oct 7, 2024 · 713679f · 713679f
1 parent 84be95e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: SigGenes
 Title: Automated differential analysis and signature generation for bulk and single-cell data
 Description: Automated differential analysis between groups based on limma-voom and generation of per-group signatures via custom filtering.
-Version: 1.0.5
+Version: 1.0.6
 Author: Alexander Bender [aut,cre]
 Maintainer: Alexander Bender <[email protected]>
 License: LGPL (>=2)

diff --git a/NEWS b/NEWS
@@ -1,7 +1,13 @@
+CHANGES IN VERSION 1.0.6
+------------------------
+
+    o retire unused argument in `de_testing()`
+
+
 CHANGES IN VERSION 1.0.5
 ------------------------
 
-    o option to use limma-trend for testing rather than default limma-voom
+    o support to use limma-trend for testing via `use_trend=TRUE`
 
 
 CHANGES IN VERSION 1.0.4

diff --git a/R/de_testing.R b/R/de_testing.R
@@ -84,7 +84,7 @@
 #' @export
 de_limma <- function(x, use_assay = "counts", aggregate_by = NULL, use_existing_sf = TRUE,
                      main_covariate, other_covariates = NULL,
-                     test_method = c("trend", "voom"), block = NULL,
+                     block = NULL,
                      min_pct = 0, min_fc = 1.0, use_weights = FALSE,
                      mode = c("pairwise", "average"), use_trend = FALSE,
                      use_filterByExpr = FALSE, return_object = FALSE, delim = "_vs_") {

diff --git a/man/de_limma.Rd b/man/de_limma.Rd