adjacency matrix, a square, symmetric matrix with entries between 0 and 1.
colors
module labels. A vector of length ncol(adjMat) giving a module label for each
gene (node) of the network.
scaleByMax
logical: should intramodular connectivities be scaled by the maximum IM connectivity
in each module?
Value
A data frame with 4 columns giving the total connectivity, intramodular connectivity, extra-modular
connectivity, and the difference of the intra- and extra-modular connectivities for all genes.
Details
The module labels can be numeric or character. For each node (gene), the function sums adjacency
entries (excluding the diagonal) to other nodes within the same module. Optionally, the connectivities
can be scaled by the maximum connectivy in each module.
References
Dong J, Horvath S (2007) Understanding Network Concepts in Modules, BMC Systems Biology
2007, 1:24