writeScaffold: Writes the scaffold network to a sif file (with attributes)...

In cokelaer/CellNOptR: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Description

This function writes a cytoscape SIF file for the scaffold network, with an associated edge attribute file that holds whether the edge is present at t1,t2 or not present at all and another associated edge attribute file that holds the weights of the edges. This function also writes a dot file that contains the same information (see writeDot for more information about the dot file conventions).

Usage

writeScaffold(modelComprExpanded, optimResT1, optimResT2, modelOriginal,
CNOlist, tag=NULL)

Arguments

modelComprExpanded	The scaffold model (i.e. compressed and expanded)
optimResT1	The results of the optimisation process at t1
optimResT2	The results of the optimisation process at t2 (set this to NA if you have performed a one time point optimisation).
modelOriginal	The PKN model
CNOlist	The CNOlist on which the optimisation is based
tag	NULL or string; tells whether you want to prefix filenames with a tag (replaces the default behaviour).

Details

By scaffold network we mean the network that is used as a basis for optimisation (i.e. a compressed and expanded network), therefore no map back of the weights is necessary here.

The weights of the edges are computed as the mean across models within the relative tolerance limits, as output in the results from the optimisation $stringsTol. Strings that are in $stringsTol are the ones that are within the relative tolerance limits around the best solution in the population across all generations of the optimisation.

!If there is no time 2, then the argument optimResT2 should be = NA.

Value

This function does not return anything, it writes a sif file and 2 edge attributes files, and a dot file, in your working directory.

Author(s)

C.Terfve

See Also

writeNetwork, writeDot

Examples

tmpdir<-tempdir()
setwd(tmpdir)

#load the data

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

#pre-process the model (partial)

indicesToy<-indexFinder(CNOlistToy,ToyModel,verbose=TRUE)
ToyNCNOcutComp<-compressModel(ToyModel,indicesToy)
indicesToyNCNOcutComp<-indexFinder(CNOlistToy,ToyNCNOcutComp)
ToyNCNOcutCompExp<-expandGates(ToyNCNOcutComp)

#optimise

ToyFields4Sim<-prep4sim(ToyNCNOcutCompExp)
initBstring<-rep(1,length(ToyNCNOcutCompExp$reacID))
ToyT1opt<-gaBinaryT1(
	CNOlist=CNOlistToy,
	model=ToyNCNOcutCompExp,
	initBstring=initBstring, 
	maxGens=3,
	popSize=5,
	verbose=TRUE)

#write the network

writeScaffold(
	modelOriginal=ToyModel,
	modelComprExpanded=ToyNCNOcutCompExp,
	optimResT1=ToyT1opt,
	optimResT2=NA,
	CNOlist=CNOlistToy)

cokelaer/CellNOptR documentation built on May 27, 2019, 8:44 a.m.