simulateNetwork: Simulated networks

Description Usage Arguments Value Examples

View source: R/ALPACAFunctions.R

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

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simulateNetwork(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

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meghapadi/ALPACA documentation built on Oct. 20, 2017, 6:40 a.m.