write_constraints: Writing the set of constraints for the ILP implementation of...

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

Description

This function takes as input the integer variables assigned to each of the elements in the network and data in a CNOlist object in order to produce the set of constraints needed to be optimized by the ILP solver.

Usage

write_constraints <- function(model,
                              midasExperimentPart,
                              midasTreatmentPart,
                              reaction_sets,
                              y_vector, 
                              midas, 
                              binary_variables)

Arguments

model	the model
midasExperimentPart	the experimental part of CNOlist where data is stored
midasTreatmentPart	the treatment part of CNOlist where data is stored
reaction_sets	the set of reactions
y_vector	the variables for each interaction in the PKN
midas	the midas table
binary_variables	the set of binary variables

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.

CellNOptR documentation built on Nov. 8, 2020, 6:58 p.m.