CellNOptR (version 1.18.0)

compressModel: 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.

Value

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

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.

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)