From e28b8d1ef9bb1f25f7b8263c0851f5940fc19faa Mon Sep 17 00:00:00 2001
From: Benjamin James <benjames@mit.edu>
Date: Wed, 30 Oct 2024 16:55:31 -0400
Subject: [PATCH] Keep independent filtering on by default

---
 R/deg.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/deg.R b/R/deg.R
index dacd6c8..2d18129 100644
--- a/R/deg.R
+++ b/R/deg.R
@@ -486,7 +486,7 @@ deg.deseq2 <- function(se,
                        case,
                        control,
                        sample.col,
-                       covariates=NULL, independentFiltering=as.logical(Sys.getenv("DESEQ2_INDEPENDENT", "FALSE")=="TRUE"),
+                       covariates=NULL, independentFiltering=as.logical(Sys.getenv("DESEQ2_INDEPENDENT", "TRUE")=="TRUE"),
                        prefix="DESeq2") {
     pb = calculate_qc_metrics(se_make_pseudobulk(se, sample.col), assay="counts", qc_vars=c("mt", "ribo", "pc", "chrX", "chrY"))
     X = SummarizedExperiment::assays(pb)$counts