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| author | Alexander Kabui | 2021-09-14 22:31:18 +0300 |
|---|---|---|
| committer | Alexander Kabui | 2021-09-14 22:31:18 +0300 |
| commit | 49fdd614d4b18f7d28126e4ebbf3adca57f0416f (patch) | |
| tree | c7b5e72fa522998305fe602df38026dd42f176fb | |
| parent | ea0e92d3f63a9f403aacd5ab1590f61f2752158a (diff) | |
| download | genenetwork3-49fdd614d4b18f7d28126e4ebbf3adca57f0416f.tar.gz | |
Checking data for excessive missing values
| -rw-r--r-- | scripts/wgcna_analysis.R | 20 |
1 files changed, 19 insertions, 1 deletions
diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R index a8170b6..8e90d7d 100644 --- a/scripts/wgcna_analysis.R +++ b/scripts/wgcna_analysis.R @@ -10,10 +10,28 @@ wgcnaRawData <- read.csv(file = "wgcna_data.csv") # transform expressionData -datExpr <- as.data.frame(t(wgcnaRawData)); +dataExpr <- as.data.frame(t(wgcnaRawData)); +# data cleaning + +# adopted from docs +gsg = goodSamplesGenes(dataExpr, verbose = 3); + + + +if (!gsg$allOK) +{ +# Optionally, print the gene and sample names that were removed: +if (sum(!gsg$goodGenes)>0) +printFlush(paste("Removing genes:", paste(names(datExpr0)[!gsg$goodGenes], collapse = ", "))); +if (sum(!gsg$goodSamples)>0) +printFlush(paste("Removing samples:", paste(rownames(datExpr0)[!gsg$goodSamples], collapse = ", "))); +# Remove the offending genes and samples from the data: +dataExpr <- dataExpr[gsg$goodSamples, gsg$goodGenes] +} + |