create_binaries: Defining the set of binary variables for the ILP...

In saezlab/CellNOptR: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Defining the set of binary variables for the ILP implementation of CellNOptR.

Description

This function takes as input the model and data in a CNOlist object in order to define the set of binary variablese.

Usage

create_binaries(model, 
                            midas, 
                            numberOfExperiments, 
                            y_vector)

Arguments

model	the model
midas	the midas table
numberOfExperiments	the number of experimental conditions
y_vector	the variables for each interaction in the PKN

Author(s)

E Gjerga, H Koch

References

Alexander Mitsos, Ioannis N. Melas, Paraskeuas Siminelakis, Aikaterini D. Chairakaki, Julio Saez-Rodriguez, and Leonidas G. Alexopoulos. Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data. PLoS Comput Biol. 2009 Dec; 5(12): e1000591.

saezlab/CellNOptR documentation built on April 16, 2024, 5:21 a.m.