From 9c221e0d89603acd5412be95650a469824e2ab99 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 15:10:16 +0300
Subject: check for na powerEst and use a default value

---
 scripts/wgcna_analysis.R | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index ee749e9..c3b1ac8 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -62,13 +62,21 @@ enableWGCNAThreads()
 powers <- c(c(1:10), seq(from = 12, to=20, by=2)) 
 sft <- pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
 
+# check the power estimate
+
+if (is.na(sft$powerEstimate)){
+  powerEst = 1
+}else{
+  powerEst = sft$powerEstimate
+}
+
 # pass user options
 network <- blockwiseModules(dataExpr,
                   #similarity  matrix options
                   corType = corType,
                   #adjacency  matrix options
 
-                  power = 5,
+                  power = powerEst,
                   networkType = "unsigned",
                   #TOM options
                   TOMtype =  TOMtype,
-- 
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