WGCNA export network into cytoscape : problem

Question

[ASid]

The threshold (which corresponds to adjacency threshold for including edges in the output.) in the function “exportNetworkToCytoscape” (WGCNA) affects the results in which manner? I wanted to export the network of 461 module size into cutoscape network format and it gave me the 447 nodes in the resultant network when I used threshold =0.02 . Why this number was reduced from 461 to 447? What does this value does to the node numbers in module when exported ? I used the code:

cyt = exportNetworkToCytoscape(modTOM,
                               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,
                               nodeAttr = moduleColors[inModule]);

[Jean-Karim Heriche]

It could be that the function discards singletons (i.e. unconnected nodes) after thresholding.

[WouterDeCoster]

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