compressModel {CellNOptR} | R Documentation

## Compress a model

### Description

This function compresses a model by compressing species that are not signals/inhibited/stimulated and that are not dead ends/in complex logic (i.e. only species with either one input or one output are compressed)/in self loops.

You can also use preprocessing function instead that calls compressModel and other preprocessing functions.

### Usage

    compressModel(model, indexes)

### Arguments

`model` | a model structure as produced by readSIF.
`indexes` | list of indexes of the species stimulated/inhibited/measured in the model, as created by indexFinder.

### Details

Be aware that in the multiple inputs/one output case, if one of the outputs is an '&' gate this function handles it fine as long as it is an '&' with 2 inputs and no more.

### Value

a compressed model list, with an additional field called 'speciesCompressed' that contains the names of the species that have been compressed

### Note

No need to call this function directly since version 0.99.24. Use preprocessing instead.

### Author(s)

C. Terfve

### See Also

indexFinder, readSIF, preprocessing

### Examples

    #load data

    data(CNOlistToy,package="CellNOptR")
    data(ToyModel,package="CellNOptR")

    indicesToy<-indexFinder(CNOlistToy,ToyModel,verbose=FALSE)
    toyComp<-compressModel(ToyModel,indicesToy)

[Package CellNOptR version 1.40.0 Index]