alpacaSimulateNetwork: Simulated networks

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

Simulated networks

Description

This function creates a pair of networks given user-defined parameters for the modular structure of the first (healthy) network and the type of added module in the second (disease) network.

Usage

alpacaSimulateNetwork(
  comm.sizes,
  edge.mat,
  num.module,
  size.module,
  dens.module
)

Arguments

comm.sizes	A two-column matrix indicating the number of "from" nodes (left column) and number of "to" nodes (right column) in each community (row).
edge.mat	A matrix indicating the number of edges from the TFs in community i (rows) to target genes in community j (columns).
num.module	The number of modules that will be added to simulate the disease network.
size.module	A two-column matrix indicating the number of "from" and "to" nodes in each new module (row) that will be added to simulate the disease network.
dens.module	A vector of length num.module, indicating the edge density of each added module.

Value

A list with two elements. The first element is a four-column edge table of the same form that is input into the differential modularity function. The second element is a list of all the new nodes in the modules that were added to create the disease network.

Examples

a <- 1 # example place holder

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.