From e0084ef210fed347461427357a065b053a2d67ba Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Fri, 19 Feb 2021 08:25:31 +0100
Subject: [PATCH 1/2] fix pseudocount in FindMarkers.Assay

---
 R/differential_expression.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/differential_expression.R b/R/differential_expression.R
index 3abf832e9..5566004c0 100644
--- a/R/differential_expression.R
+++ b/R/differential_expression.R
@@ -627,6 +627,7 @@ FindMarkers.Assay <- function(
     cells.1 = cells.1,
     cells.2 = cells.2,
     features = features,
+    pseudocount.use = pseudocount.use,
     mean.fxn = mean.fxn,
     fc.name = fc.name,
     base = base

From 3863336fa3e0fc5e1698879e0c3505e084de8345 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Fri, 19 Feb 2021 08:26:04 +0100
Subject: [PATCH 2/2] fix mean.fxn and fc.name in FindMarkers.DimReduc

---
 R/differential_expression.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/R/differential_expression.R b/R/differential_expression.R
index 5566004c0..60cba62f8 100644
--- a/R/differential_expression.R
+++ b/R/differential_expression.R
@@ -681,6 +681,7 @@ FindMarkers.DimReduc <- function(
   min.cells.group = 3,
   pseudocount.use = 1,
   mean.fxn = rowMeans,
+  fc.name = NULL,
   ...
 
 ) {
@@ -706,7 +707,9 @@ FindMarkers.DimReduc <- function(
     object = object,
     cells.1 = cells.1,
     cells.2 = cells.2,
-    features = features
+    features = features,
+    mean.fxn = mean.fxn,
+    fc.name = fc.name
   )
   # subsample cell groups if they are too large
   if (max.cells.per.ident < Inf) {