writeObjectiveFunction {CellNOptR} | R Documentation

## Writing the objective function 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 objective function needed to be optimized by the ILP solver.

### Usage

    writeObjectiveFunction(model,
                                       midasExperimentPart,
                                       y_vector=y_vector,
                                       accountForModelSize = TRUE,
                                       sizeFac = .000001,
                                       meansOfMeasurements_at_t0,
                                       method = "quadratic" )

### Arguments

`model` | the model
`midasExperimentPart` | the experimental part of CNOlist where data is stored
`y_vector` | the variables for each interaction in the PKN
`accountForModelSize` | the verbose variable if we wish to apply the size penalty
`sizeFac` | the size penalty factor
`meansOfMeasurements_at_t0` | the means of measurements at time-point 0
`method` | the method of defining the objective function ("quadratic/linear")

### 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.

[Package CellNOptR version 1.40.0 Index]