From 42c120dff2b3cac8a6b6546ebab9daf021aac11a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 22:42:43 +0300
Subject: compute the softthreshhold

---
 scripts/wgcna_analysis.R | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 8e90d7d..cb93492 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -5,15 +5,12 @@ stringsAsFactors = FALSE
 
 # load expression data **assumes csv format row(traits)(columns info+samples)
 
-
 wgcnaRawData <- read.csv(file = "wgcna_data.csv")
 
 # transform expressionData
 
 dataExpr <- as.data.frame(t(wgcnaRawData));
 
-
-
 # data cleaning
 
 # adopted from docs
@@ -32,6 +29,17 @@ printFlush(paste("Removing samples:", paste(rownames(datExpr0)[!gsg$goodSamples]
 dataExpr <- dataExpr[gsg$goodSamples, gsg$goodGenes]
 }
 
+# network constructions and modules
+
+# 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)
+
+
+
+
+
 
 
 
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