Getting data from TOM matrix (WGCNA)
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?
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