From 1c98a10bf5015a85b856f9e937417d51ec05d781 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 22:49:43 +0300
Subject: construct  gene co-expression  network & module detection

---
 scripts/wgcna_analysis.R | 23 ++++++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

(limited to 'scripts/wgcna_analysis.R')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index cb93492..29f0259 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -33,9 +33,26 @@ dataExpr <- dataExpr[gsg$goodSamples, gsg$goodGenes]
 
 # choose softthreshhold (Calculate soft threshold if the user specified the)
 
-powers = c(c(1:10), seq(from = 12, to=20, by=2)) 
-sft = pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
-
+powers <- c(c(1:10), seq(from = 12, to=20, by=2)) 
+sft <- pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
+
+# pass user options
+network <- blockwiseModules(dataExpr,
+                  #similarity  matrix options
+                  corType = "pearson",
+                  #adjacency  matrix options
+
+                  power = sft$powerEstimate,
+                  networkType = "unsigned",
+                  #TOM options
+                  TOMtype =  "unsigned",
+
+                  #module indentification
+
+                  minmodulesSize = 30,
+                  deepSplit = 5,
+                  PamRespectsDendro = FALSE
+                )
 
 
 
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