networkmatrix: Creates a network matrix for `pnea`

Description

Internal function, creates a two-column network matrix that can be further processed by pnea.

Usage

networkmatrix(network, nodes, nettype)

Arguments

network

One of the following objects: an adjacency matrix (class "matrix"), a sparse adjacency matrix (class "dgCMatrix") or an igraph graph (class "igraph")

nodes

Vector containing the (ordered) names of all nodes in the network

nettype

Either 'directed' or 'undirected'

Value

A two-column matrix, where every row represents and edge. For directed networks, parent nodes must be in the first column, and child nodes in the second.

Details

This is an internal function, that is called within pnea to convert different types of network objects (see argument 'network' above) into a standard two-column network matrix, that can then be processed by pnea.

Examples

Run this code

# First case: adjacency matrix
n<-50
adjacency <- matrix(sample(0:1, n^2, replace=TRUE, prob=c(0.9,0.1)), ncol=n)
diag(adjacency) <- 0
lab = paste(rep('gene'),1:n)
head(networkmatrix(adjacency, lab, 'directed'))

# Second case: sparse adjacency matrix
library(Matrix)
sparse_adjacency<-Matrix(adjacency,sparse=TRUE)
head(networkmatrix(sparse_adjacency, lab, 'directed'))

# Third case: igraph object
library(igraph)
igraph_graph = erdos.renyi.game(15, 1/3)
lab = paste(rep('gene'),1:15)
head(networkmatrix(igraph_graph, lab, 'directed'))