In WGCNA there are 3 major steps:
- Correlation calculation between genes
- Adjacency matrix generation by raising correlation matrix to power β (soft threshold)
- TOM based dissimilarity matrix generation for identifying modules/clusters
If I understand correctly, β is selected such that the resulting network fits scale-free topology. Till step 2, we will have all-to-all connection between the genes. The adjacency matrix in step 2 gives for the weight for each edge. At this stage how does it select which edges to retain in the final network?