CellNOptR: compressModel – R documentation

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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.

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

Examples

#load data

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

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

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