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authorAlexander Kabui2021-09-27 15:15:28 +0300
committerAlexander Kabui2021-09-27 15:15:28 +0300
commit6f25b8e2b1d1a34c054d325b1c37b303529b8827 (patch)
treef067038677002555325af043a0ecd300e984003d /scripts/wgcna_analysis.R
parent7dbb0e6d27cdb0923e94685cf44d244dd8a2e105 (diff)
downloadgenenetwork3-6f25b8e2b1d1a34c054d325b1c37b303529b8827.tar.gz
remove unnecessary comments and variables
Diffstat (limited to 'scripts/wgcna_analysis.R')
-rw-r--r--scripts/wgcna_analysis.R18
1 files changed, 4 insertions, 14 deletions
diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index e641652..17b3537 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -23,24 +23,14 @@ if (length(args)==0) {
inputData <- fromJSON(file = json_file_path)
-# parse the json data input
-
-minModuleSize <-inputData$minModuleSize
-
-TOMtype <-inputData$TOMtype
-
-corType <-inputData$corType
-#
-
trait_sample_data <- do.call(rbind, inputData$trait_sample_data)
dataExpr <- data.frame(apply(trait_sample_data, 2, function(x) as.numeric(as.character(x))))
# transform expressionData
dataExpr <- data.frame(t(dataExpr))
-gsg = goodSamplesGenes(dataExpr, verbose = 3);
+gsg = goodSamplesGenes(dataExpr, verbose = 3)
-# https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/
if (!gsg$allOK)
{
if (sum(!gsg$goodGenes)>0)
@@ -75,18 +65,18 @@ if (is.na(sft$powerEstimate)){
# pass user options
network <- blockwiseModules(dataExpr,
#similarity matrix options
- corType = corType,
+ corType = inputData$corType,
#adjacency matrix options
power = powerEst,
networkType = "unsigned",
#TOM options
- TOMtype = TOMtype,
+ TOMtype = inputData$TOMtype,
#module indentification
verbose = 3,
- minmodulesSize = minModuleSize,
+ minmodulesSize = inputData$minModuleSize,
deepSplit = 3,
PamRespectsDendro = FALSE
)