From 27d54257735156ebc9d12f3ce638ea469d14e15e Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 22 Dec 2021 09:40:15 +0300
Subject: Refactor wgcna (#63)

* add r as a gn3 input

* calculate powers from user input

* fix merge conflict---
 scripts/wgcna_analysis.R | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

(limited to 'scripts/wgcna_analysis.R')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index b0d25a9..d368013 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -25,6 +25,7 @@ if (length(args)==0) {
 inputData <- fromJSON(file = json_file_path)
 imgDir = inputData$TMPDIR
 
+inputData
 
 trait_sample_data <- do.call(rbind, inputData$trait_sample_data)
 
@@ -51,10 +52,8 @@ names(dataExpr) = inputData$trait_names
 # Allow multi-threading within WGCNA
 enableWGCNAThreads()
 
-# choose softthreshhold (Calculate soft threshold)
-# xtodo allow users to pass args
-
-powers <- c(c(1:10), seq(from = 12, to=20, by=2)) 
+# powers <- c(c(1:10), seq(from = 12, to=20, by=2)) 
+powers <- unlist(c(inputData$SoftThresholds))
 sft <- pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
 
 # check the power estimate
-- 
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