From 96dcf6877b033ff03814c942f7855f152f59bfaf Mon Sep 17 00:00:00 2001
From: Benjamin James <benjames@mit.edu>
Date: Fri, 9 Feb 2024 11:54:29 -0500
Subject: [PATCH] null reduction

---
 R/deg.R | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/R/deg.R b/R/deg.R
index 05652a2..75422b6 100644
--- a/R/deg.R
+++ b/R/deg.R
@@ -92,7 +92,12 @@ deg.dysregulation <- function(sce, pathology, sample.col, covariates=NULL,  verb
     cd = SummarizedExperiment::colData(pb)
     if (attr(pb, "class") == "SingleCellExperiment") {
         rd = SingleCellExperiment::reducedDims(sce)[[reduction]]
-        X = t(rd)
+        if (!is.null(rd)) {
+            X = t(rd)
+        } else {
+            pb = se_tmm(pb, log=TRUE)
+            X = SummarizedExperiment::assays(pb)$TMM
+        }
     } else {
         pb = se_tmm(pb, log=TRUE)
         X = SummarizedExperiment::assays(pb)$TMM