Keep independent filtering on by default

KellisLab · Oct 30, 2024 · e28b8d1 · e28b8d1
1 parent 05ef111
commit e28b8d1
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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