CellNOptR: write_constraints – R documentation

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write_constraints

Writing the set of constraints for the ILP implementation of CellNOptR.

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

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

v1.36.0

GPL-3

Authors

T.Cokelaer, F.Eduati, A.MacNamara, S.Schrier, C.Terfve, E.Gjerga, A.Gabor

Initial release

2018-11-08