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Question: problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
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gravatar for modarzi
10 weeks ago by
modarzi10
modarzi10 wrote:

Hi,

I run WGCNA for my study.Now, I want to import my network in Cytoscape for visualization. based on WGCNA tutorial, for that purpose I have to run below code:

    # select modules modules = c("blue","brown") 
    # Select module probes 
    inModule=is.finite(match(moduleColorsFemale,modules)) 
    modProbes=probes[inModule] 
    match1=match(modProbes,GeneAnnotation$substanceBXH) 
    modGenes=GeneAnnotation$gene_symbol[match1] 
    # Select the corresponding Topological Overlap 
     modTOM = TOM[inModule, inModule] 
    dimnames(modTOM) = list(modProbes, modProbes) 
    # Export the network into edge and node list files for Cytoscape 
    cyt = exportNetworkToCytoscape(modTOM, 
    edgeFile=paste("CytoEdge",paste(modules,collapse="-"),".txt",sep=""), nodeFile=paste("CytoNode",paste(modules,collapse="-"),".txt",sep=""), 
    weighted = TRUE, threshold = 0.02,nodeNames=modProbes, 
    altNodeNames = modGenes, nodeAttr = moduleColorsFemale[inModule])

when I want to run:

modTOM = TOM[inModule, inModule]  

I got below error:

Error: object 'TOM' not found.

So, my question is what is TOM.should I calculate TOM via below code:

> TOM = TOMsimilarityFromExpr(datExpr, power=7)
 
I appreciate if anybody share his/her comment with me.

 

Best Regrds,

Mohammad

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by modarzi10
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