From 6f3ce5f28855920e1eb63bd998f0dfa61bd73518 Mon Sep 17 00:00:00 2001
From: atpoint <atpoint90@gmail.com>
Date: Fri, 6 Dec 2024 14:34:09 +0100
Subject: [PATCH] also return weights

---
 DESCRIPTION    | 2 +-
 NEWS           | 5 +++++
 R/de_testing.R | 2 ++
 3 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5defe36..0430782 100644
--- 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: 1.0.7
+Version: 1.0.8
 Author: Alexander Bender [aut,cre]
 Maintainer: Alexander Bender <atpoint90@gmail.com>
 License: LGPL (>=2)
diff --git a/NEWS b/NEWS
index fc914fd..df9e589 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,8 @@
+CHANGES IN VERSION 1.0.8
+------------------------
+
+    o if returning the DGEList also add weights if estimated
+
 CHANGES IN VERSION 1.0.7
 ------------------------
 
diff --git a/R/de_testing.R b/R/de_testing.R
index c3b655a..18f648c 100644
--- a/R/de_testing.R
+++ b/R/de_testing.R
@@ -231,6 +231,7 @@ de_limma <- function(x, use_assay = "counts", aggregate_by = NULL, use_existing_
     aw <- NULL
     if (use_weights) {
       aw <- arrayWeights(object = lcpm, design = design)
+
     }
 
     if (!is.null(block)) {
@@ -312,6 +313,7 @@ de_limma <- function(x, use_assay = "counts", aggregate_by = NULL, use_existing_
   to_return <- SimpleList(results = de_results)
 
   if (return_object) {
+    pb$samples$weights <- aw
     to_return[["DGEList"]] <- pb
   }