Nothing
getWGCNANet <-
function (DEGeneExpr,SoftThreshold=8,AThreshold=0.85,AddAnnotations=F,MartDataset="hsapiens_gene_ensembl")
{
optionValue<-getOption("stringsAsFactors")
options(stringsAsFactors=F)
CorrelationVals<-computeSimilarities(DEGeneExpr)
Correlations<-CorrelationVals$Correlations
PValues<-CorrelationVals$PValues
Similarities<-CorrelationVals$Similarities
rm(CorrelationVals)
AdjacencyScores=1/(1+exp(-SoftThreshold*(Similarities-0.5)))
AdjacencyScores[which(AdjacencyScores<AThreshold & AdjacencyScores>(1-AThreshold))]<-0
AdjacencyScores[lower.tri(AdjacencyScores,diag=T)]<-0
GenesAnnotations <- NULL
if (AddAnnotations)
{
cat("Adding annotations...\n")
if (requireNamespace("biomaRt",quietly=TRUE)) {ensembl <- biomaRt::useMart("ensembl", dataset = MartDataset)} else {stop("biomaRt package must be installed to use this function")}
GenesAnnotations <- getGenesInformations(rownames(AdjacencyScores),ensembl)
}
WGCNANetwork<-WGCNANet(AdjacencyScores,SoftThreshold,AThreshold,Correlations,PValues,DEGeneExpr,GenesAnnotations)
options(stringsAsFactors=optionValue)
return(WGCNANetwork)
}
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