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Diffstat (limited to 'scripts/wgcna_analysis.R')
| -rw-r--r-- | scripts/wgcna_analysis.R | 14 |
1 files changed, 11 insertions, 3 deletions
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) + + + + + |