newTopNetwork {RegEnrich} | R Documentation

## TopNetwork object creator

### Description

This function create 'TopNetwork' object using 3-column edge table.

### Usage

    newTopNetwork(
      networkEdgeTable,
      reg = "",
      directed = TRUE,
      networkConstruction = c("new", "COEN", "GRN"),
      percent = 100
    )

### Arguments

`networkEdgeTable` | a data frame of 3 columns, representing 'from.gene' ('regulators'), 'to.gene' ('targets') and 'weight', respectively.
`reg` | a vector of gene regulators.
`directed` | logical, whether the network is directed. Default is TRUE.
`networkConstruction` | the method to construct this network. Possible can be: 'COEN', coexpression network; 'GRN', gene regulatory network by random forest; 'new' (default), meaning a network provided by user, rather than infered based on the expression data.
`percent` | the percentage of edges in the original whole network. Default is 100, meaning 100% edges in whole network.

### Value

an object of topNetwork class.

### Examples

    data(TFs)
    edge = data.frame(from = rep(TFs$TF_name[seq(3)], seq(3)),
                      to = TFs$TF_name[11:16], weight = 0.1*(6:1))
    object = newTopNetwork(edge, networkConstruction = 'new', percent = 100)
    object
    str(object)

[Package RegEnrich version 1.2.0 Index]