From 24eba66fb3486f504bef767180cf436bfb54d318 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Fri, 22 Dec 2023 10:50:09 -0800
Subject: [PATCH] fill na related to #12

---
 screenpro/phenoScore.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/screenpro/phenoScore.py b/screenpro/phenoScore.py
index 59553d7..e95936f 100644
--- a/screenpro/phenoScore.py
+++ b/screenpro/phenoScore.py
@@ -60,7 +60,7 @@ def runPhenoScore(adata, cond1, cond2, math, test, score_level,
         # Calculate the adjusted p-values using the Benjamini-Hochberg method
         if p_values is None:
             raise ValueError('p_values is None')
-        _, adj_pvalues, _, _ = multipletests(p_values, alpha=0.05, method='fdr_bh')
+        _, adj_pvalues, _, _ = multipletests(p_values.fillna(1), alpha=0.05, method='fdr_bh')
         # get targets
         targets = adata.var.index.str.split('_[-,+]_').str[0].to_list()
         # combine results into a dataframe