newTopNetwork: TopNetwork object creator

In RegEnrich: Gene regulator enrichment analysis

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)

RegEnrich documentation built on March 7, 2021, 2 a.m.