mapBTables2model: Integrate Boolean tables with the model

In saezlab/CNORfeeder: Integration of CellNOptR to add missing links

Integrate Boolean tables with the model

Description

This function infers the network from the Boolean tables and integrates it with the network encoded in the model (generally derived from prior knowledge), adding links that are missing.

Usage

mapBTables2model(BTable,model,optimRes=NA,allInter=TRUE,compressed=TRUE)

Arguments

BTable	a BTable list, as created by makeBTables
model	a model list, as created by readSif
optimRes	a bit string with the reaction of the model to be considered, default considers all reactions
allInter	one new link in the network can correspond to more links in the model, set it to TRUE if you want to add all possible links, FALSE to add only one link, default is TRUE
compressed	this argument is used to decede how to deal with unmeasured and unperturbed nodes (white nodes). As general guideline, it should be set to TRUE if the PKN has been compressed in the preprocessing step, FALSE otherwise. Default is TRUE.

Details

The function receive as input the Boolean Tables, infers the data-driven network form them (as descibed in (Eduati et al., PLoS ONE, 2010)) and integrates it with the model, returning a new model with the integrated links. If the Model is not given as input (Model=NULL), the data-driven network is returned as model.

Value

a new model with the integrated links and an additional field:

indexIntegr

a vector with the indexes of the integrated links

Author(s)

F.Eduati

References

F. Eduati, A. Corradin, B. Di Camillo, G. Toffolo. A Boolean approach to linear prediction for signaling network modeling. PLoS ONE; 5(9): e12789.

See Also

readSif, readMIDAS, makeBTables

Examples

data(CNOlistDREAM,package="CellNOptR")
data(DreamModel,package="CellNOptR")
model<-preprocessing(data=CNOlistDREAM, model=DreamModel)
BTable <- makeBTables(CNOlist=CNOlistDREAM, k=2, measErr=c(0.1, 0))
modelIntegr <- mapBTables2model(BTable=BTable,model=model,allInter=TRUE)
# modelIntegr$reacID[modelIntegr$indexIntegr] to see the integrated links

saezlab/CNORfeeder documentation built on Feb. 14, 2023, 3:23 p.m.