I'm using the Weighted Gene Coexpression Network Analysis package (WGCNA) in R and I am trying to figure out how the adjacency matrix is defined.
I understand how the correlation matrix is created along with why the power is used but adjacency matrices should be either 1 or 0.
Why are there still continuous values? How does it choose a cutoff later?
I can understand that it's maybe a weighted adjacency matrix but there isn't an option to make it binary and that is needed for the topological overlap matrix calculation (TOM)