Entering edit mode
4.5 years ago
yearn.nexus
•
0
I want to choose top 20 hub genes to visualize in the cytoscape,but the hub gene was lost, there are only 19 genes in my export files. Here is my codes :
modules = c("lightcyan")
probes = names(datExpr0)
inModule = is.finite(match(moduleColors, modules));
modProbes = probes[inModule];
modGenes = annot$description[match(modProbes, annot$GeneID)]
modTOM = TOM[inModule, inModule]
dimnames(modTOM) = list(modProbes, modProbes)
nTop = 20
IMConn = softConnectivity(datExpr0[, modProbes]);
top = (rank(-IMConn) <= nTop)
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 = modProbes,
altNodeNames = modGenes,
nodeAttr = moduleColors[inModule])
I tried different modules ,but the outcomes only had 19 genes, the lost one was always hub gene, I have no idea what to do next,someone can help me ?
whats your threshold?