expandGates {CellNOptR} | R Documentation |
This function takes in a model and splits all AND gates into ORs. In addition, wherever there are more than one, it creates all possible ANDs combinations of them, but considering only ANDs with 2, 3 or 4 inputs according to the user argument (default is 2)
expandGates(model, ignoreList=NA, maxInputsPerGate=2)
model |
a model structure |
ignoreList |
a list of reactions indices to ignore |
maxInputsPerGate |
maximum number of input per gates (Default is 2; up to 4) |
This function returns a model with additional fields that help keep track of the processing done on the network. I would advice not to overwrite on the initial model but rather to assign the result of this function to a variable with a different name.
returns a model, with additional fields:
SplitANDs |
list that contains a named element for each AND reac that has been split, and each element contains a vector with the names of the of the reactions that result from the split if nothing was split, this element has the default value $initialReac [1] "split1" "split2" |
newANDs |
list that contains an element for each new '&' gate, named by the name of this new and reac, and containing a vector of the names of the reactions from which it was created (contains all the reacs in that pool, not the particular ones, this could be improved) |
No need to call this function directly since version 0.99.24. Use preprocessing instead.
C.Terfve. T. Cokelaer, A.MacNamara, Martin-Franz-Xaver Pirkl
#load data data(CNOlistToy,package="CellNOptR") data(ToyModel,package="CellNOptR") #pre-process the model indicesToy<-indexFinder(CNOlistToy,ToyModel,verbose=TRUE) ToyNCNOindices<-findNONC(ToyModel,indicesToy,verbose=TRUE) ToyNCNOcut<-cutNONC(ToyModel,ToyNCNOindices) indicesToyNCNOcut<-indexFinder(CNOlistToy,ToyNCNOcut) ToyNCNOcutComp<-compressModel(ToyNCNOcut,indicesToyNCNOcut) indicesToyNCNOcutComp<-indexFinder(CNOlistToy,ToyNCNOcutComp) ToyNCNOcutCompExp<-expandGates(ToyNCNOcutComp, maxInputsPerGate=4)