From 44ca6954fbd42af50f1bc5ed7c02a85bdb98f6f1 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Fri, 22 Dec 2023 10:56:42 -0800
Subject: [PATCH] fill na pvalues with 1 related to #12

---
 screenpro/phenoScore.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/screenpro/phenoScore.py b/screenpro/phenoScore.py
index e95936f..3508ee9 100644
--- a/screenpro/phenoScore.py
+++ b/screenpro/phenoScore.py
@@ -56,11 +56,12 @@ def runPhenoScore(adata, cond1, cond2, math, test, score_level,
             math=math, ave_reps=True, test=test, 
             growth_rate=growth_rate
         )
-
+        # fill na with 1
+        p_values[np.isnan(p_values)] = 1
         # 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.fillna(1), alpha=0.05, method='fdr_bh')
+        _, adj_pvalues, _, _ = multipletests(p_values, alpha=0.05, method='fdr_bh')
         # get targets
         targets = adata.var.index.str.split('_[-,+]_').str[0].to_list()
         # combine results into a dataframe