Getting data from TOM matrix (WGCNA)
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Entering edit mode
9 weeks ago
cgias ▴ 20

Hello,

I would like to access the correlation in TOM matrix of a specific subset of genes. Manually, as it is a matrix, there're no row/column names so I can't identify the genes I'm looking for.

In the manual, I've seen the function

subsetTOM(
  datExpr, 
  subset,
  corFnc = "cor", corOptions = "use = 'p'", 
  weights = NULL,  
  networkType = "unsigned", 
  power = 6, 
  verbose = 1, indent = 0)

but I couldn't figure out what is the "subset" object and haven't found anything online either. It is described as

a single logical or numeric vector giving the indices of the nodes for which the TOM is to be calculated

Is it a vector of Trues and Falses for each gene, being True the ones I am looking for?

wgcna tom matrix • 100 views
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