Description Usage Arguments Value Examples

View source: R/ALPACAFunctions.R

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.

1 | ```
simulateNetwork(comm.sizes, edge.mat, num.module, size.module, dens.module)
``` |

`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. |

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.

1 |

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