Question: Problem with edgesfile into cytoscape for network plot
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gravatar for Biologist
8 weeks ago by
Biologist190
Biologist190 wrote:

I was using 30,000 protein-coding genes and lncRNAs for network construction on WGCNA. I have got 25 modules. And I'm interested in creating a network plot. I see that everyone is using cytoscape. So, I got the edges and nodes files with the following commands.

genes = colnames(datExpr)
dimnames(TOM) <- list(genes, genes)
module_colors2= dynamicColors[restGenes]
cyt = exportNetworkToCytoscape(TOM,
                               edgeFile = paste("samples_wgcna", ".edges.txt", sep=""),
                               nodeFile = paste("samples_wgcna", ".nodes.txt", sep=""),
                               weighted = TRUE, threshold = 0,
                               nodeNames = genes, nodeAttr = module_colors2)

I see that edges file is about 6GB. It looks very problematic to upload that in cytoscape. Not working properly. Is there any other way to make network with all the modules with genes and lncRNAs?

R rna-seq cytoscape wgcna • 113 views
ADD COMMENTlink modified 8 weeks ago by andres.firrincieli640 • written 8 weeks ago by Biologist190
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gravatar for andres.firrincieli
8 weeks ago by
andres.firrincieli640 wrote:

Hi,

just increase the threshold value

ADD COMMENTlink written 8 weeks ago by andres.firrincieli640
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