alpacaGenLouvain: Generalized Louvain optimization

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

Generalized Louvain optimization

Description

This function implements the Louvain optimization scheme on a general symmetric matrix. First, nodes are all placed in separate communities, and merged iteratively according to which merge moves result in the greatest increase in the modularity sum. Note that nodes are iterated in the order of the input matrix (not randomly) so that all results are reproducible. Second, the final community membership is used to form a alpacaMetaNetwork whose nodes represent communities from the prevous step, and which are connected by effective edge weights. The merging process is then repeated on the alpacaMetaNetwork. These two steps are repeated until the modularity sum does not increase more than a very small tolerance factor. New

Usage

alpacaGenLouvain(B)

Arguments

B	Symmetric modularity matrix

Value

The community membership vector

Examples

a <- 1 # example place holder

netZoo/netZooR documentation built on June 8, 2024, 6:20 a.m.