get_edges_from_topology_file

<p>string. The name of the .sif file (can be a full path
name).</p>

topology.file

<p>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.</p>

Analysis and visualization of an ensemble of boolean models for
biomarker discovery in cancer cell networks. The package allows to easily
import the data results of a software pipeline that predicts synergistic drug
combinations in cancer cell lines, developed by the DrugLogics research group
in NTNU. It has generic functions that can be used to split a boolean model
dataset to model groups with regards to the models predictive performance (number of true
positive predictions or Matthews correlation coefficient score) or synergy prediction based on a given set
of observed synergies and find the average activity difference per network
node between all group pairs. Thus, given user-specific thresholds,
important nodes (biomarkers) can be accessed in the sense that they make the
models predict specific synergies (synergy biomarkers) or have better
performance in general (performance biomarkers). Lastly, if the
boolean models have a specific equation form and differ only in their link operator,
link operator biomarkers can also be assessed.

get_edges_from_topology_file: Get the edges from a specified topology

Description

Usage

Arguments

Value