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

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).

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.

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.

Examples

Run this code

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)