CNORwrap: CNOR analysis wrapper

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

Description

This function is a wrapper around the whole CNOR analysis, it performs the following steps:

1. Plot the CNOlist;

2. Checks data to model compatibility;

3. Call the preprocessing function (Cut the nonc off the model, compress the model and expand the gates);

4. Compute the residual error;

5. Prepare for simulation;

6. Optimisation T1 and T2 (optional);

7. Plot simulated and experimental results;

8. Plot the evolution of fit;

9. Write the scaffold and PKN;

10. Write the report

Usage

CNORwrap(paramsList=NA, data=NA, model=NA, name, namesData=NA, time=1,
compression=TRUE, expansion=TRUE, cutNONC=TRUE)

Arguments

paramsList

A list of parameters related to the Genetic Algorithm parameters: sizeFac: default to 1e-04; NAFac: default to 1;popSize: default to 50; pMutation: default to 0.5; maxTime: default to 60; maxGens: default to 500; stallGenMax: default to 100; selPress: default to 1.2; elitism: default to 5; relTol: default to 0.1; verbose: default to FALSE (default to true in the functions used by CNORwrap but CNORwrap sets them to false by default).

and the Data and Model structure.

If paramsList is not provided (NA), it is filled internally with the defaultParameters function.

If Data and Model are not provided in paramList, the function looks for Data and Model arguments.

If Data and Model are provided, the function overwrites the field data and model in paramsList.

data	a CNOlist structure, as created by makeCNOlist
model	a model structure, as created by readSIF.
name	a string that will be used to name the project and all graphs produced
namesData	a list with two elements:CNOlist and Model, each containing a string that is a reference for the user to know which model/data set was used (it will be included in the report). If not provided, the list is built automatically using the name arguments.
time	either 1 or 2: Do you want to perform a one time point steady state optimisation or a 2 time points pseudo steady state optimisation. By default this is set to 1.
compression	compress the model (default TRUE)
expansion	expand the gates (default TRUE)
cutNONC	cut the NONC nodes off the model by (default TRUE)

Details

If you do not provide a parameters list, you can provide only essential elements, and all other parameters will be set to their default values. In this case, you should set paramsList=NA, and provide the following fields: data, model, name, time.

Value

This function does not return anything, it does the analysis, produces all the plots and puts them in a folder that is in your working directory, and is called "Name".

Author(s)

C. Terfve

Examples

#version with paramslist

tmpdir<-tempdir()
setwd(tmpdir)

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

pList = defaultParameters(CNOlistToy, ToyModel)
pList$maxGens = 5
pList$popSize = 5

CNORwrap(paramsList=pList, name="Toy",
    namesData=list(CNOlist="ToyData", model="ToyModel"))

## Not run: 
#version with default parameters

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

CNORwrap(name="Toy",
    namesData=list(CNOlist="ToyData",model="ToyModel"),
	data=CNOlistToy, model=ToyModel)

## End(Not run)

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