get_edges_from_topology_file: Get the edges from a specified topology

In emba: Ensemble Boolean Model Biomarker Analysis

Description

Use this function to read a topology .sif file (either space or tab-delimited) and get a matrix of network edges specifying the source and target name, the regulation effect (activation or inhibition) and the color (green or red) of each interaction.

Usage

get_edges_from_topology_file(topology.file)

Arguments

topology.file

string. The name of the .sif file (can be a full path name).

Value

a matrix with as many rows as in the .sif topology file (each row is an edge) and 4 columns defining the source and target node name, the regulation (activation or inhibition) and the color (green or red) of the signed interaction.

Examples

topology.file = system.file("extdata", "example.sif", package = "emba", mustWork = TRUE)
edges = get_edges_from_topology_file(topology.file)

emba documentation built on Jan. 7, 2021, 9:09 a.m.