Hi, I am trying to export network to cytoscape using WGCNA. I am selecting top 30 genes to export following the tutorial given by WGCNA authors.
In the following snippet of codes, nodeNames = modgenes selects the first 30 genes from genelist within module, not the top 30 genes. Inside the "cyt" function, modTOM[top,top] does provide right matrix with gene names, but once we export, the 30 genes are first 30 genes, not the top 30 genes. I am sure there is something that needs to be changed in "nodeNames = modgenes" section, but not sure how to address this.
<h6>#</h6>modules = "blue"
genes = names(soyseq.t)
inModule = is.finite(match(moduleColors, modules))
modgenes = genes[inModule]
modGenes = annot$TAIR[match(modgenes, annot$SoyID)]
# Select the corresponding Topological Overlap
modTOM = TOM[inModule, inModule]
dimnames(modTOM) = list(modgenes, modgenes)
nTop = 30;
IMConn = softConnectivity(soyseq.t[, modgenes]);
top = (rank(-IMConn) <= nTop)
# Export the network into edge and node list files Cytoscape can read
cyt = exportNetworkToCytoscape(modTOM[top,top],
edgeFile = paste("CytoscapeInput-edges-", paste(modules, collapse="-"), ".txt", sep=""),
nodeFile = paste("CytoscapeInput-nodes-", paste(modules, collapse="-"), ".txt", sep=""),
weighted = TRUE,
threshold = 0.02,
nodeNames = modgenes,
altNodeNames = modGenes,
nodeAttr = moduleColors[inModule])
<h6>#</h6>
Hello, I know WGCNA use TOM , the function
exportNetworkToCytoscape
needs adjacency matrix as input. It's TOM suits here?