CellNOptR: write_bounds – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

write_bounds

Writing the set of boundaries for each integer variable 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 boundaries for each integer variable.

Usage

write_bounds <- function(model,
                         midasTreatmentPart,
                         y_vector,
                         binary_variables)

Arguments

`model`	the model
`midasTreatmentPart`	the treatment part of CNOlist where data is stored
`y_vector`	the variables for each interaction in the PKN
`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