writeReport: Write a report of a CellNOptR analysis

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

Write a report of a CellNOptR analysis

Description

This function writes a short report of a CellNOptR analysis in an html page, that is linked to the various graphs produced

Usage

writeReport(modelOriginal, modelOpt, optimResT1, optimResT2, CNOlist, directory,
    namesFiles = list(dataPlot = NA, evolFitT1=NA, evolFitT2=NA, simResultsT1=NA,
    simResultsT2=NA, scaffold=NA, scaffoldDot=NA, tscaffold=NA, wscaffold=NA,
    PKN=NA, PKNdot=NA, wPKN=NA,nPKN=NA), namesData = list(CNOlist=NA, model=NA),
    resE=NULL)

Arguments

modelOriginal	the original previous knowledge network (i.e. model that you loaded) in a model list format
modelOpt	the model that was actually used for optimisation (i.e. the scaffold network, after compression and expansion) in a model list format
optimResT1	the results of the optimisation at t1, as output by gabinaryT1
optimResT2	the results of the optimisation at t2, as output by gabinaryTN. Set this to NA if you have performed a one time point optimisation.
CNOlist	a CNOlist
directory	the name of a new directory that will be created, where your results will be moved
namesFiles	a list of the names of the files that should have been created. Depending on whether a t2 optimisation was performed or not, all or some of the following fields are expected: dataPlot, evolFitT1, evolFitT2, simResultsT1, simResultsT2, scaffoldDot, scaffold, tscaffold, wscaffold, PKN, PKNdot, wPKN, nPKN.
namesData	a list with fields $CNOlist and $model that contain strings that are meaningful identifiers of your data and previous knowledge network (for your own record).
resE	a vector with named entries t1, t2 t1andt2, as produced by the function ResidualError, that contains the residual error associated with the discretisation of the data. Since version 1.3.29, there is no need to provide this argument. Kept for back compatibility.

Details

Future versions of this function might directly write and compile a tex file.

Value

This function produces a directory and moves all the files of namesFiles to it, then it creates an html report that contains infos about the optimisation process.

Author(s)

C. Terfve

See Also

writeNetwork, writeScaffold

Examples

#load data

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

#pre-process 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=2,
	popSize=5,
	verbose=TRUE)

#write report

namesFilesToy<-list(
	dataPlot=NA,
	evolFitT1=NA,
	evolFitT2=NA,
	simResultsT1=NA,
	simResultsT2=NA,
	scaffold=NA,
	scaffoldDot=NA,
	tscaffold=NA,
	wscaffold=NA,
	PKN=NA,
	PKNdot=NA,
	wPKN=NA,
	nPKN=NA)

writeReport(
	modelOriginal=ToyModel,
	modelOpt=ToyNCNOcutCompExp,
	optimResT1=ToyT1opt,
	optimResT2=NA,
	CNOlist=CNOlistToy,
	directory="testToy",
	namesFiles=namesFilesToy,
	namesData=list(CNOlist="Toy",model="ToyModel"),
	resE=NA)

saezlab/CellNOptR documentation built on April 16, 2024, 5:21 a.m.