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-rw-r--r--scripts/wgcna_analysis.R23
1 files changed, 20 insertions, 3 deletions
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
+ )