CellNOptR (version 1.18.0)

CNORwrap: CNOR analysis wrapper

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:

1. sizeFac: default to 1e-04;
2. NAFac: default to 1;popSize: default to 50;
3. pMutation: default to 0.5;
4. maxTime: default to 60;
5. maxGens: default to 500;
6. stallGenMax: default to 100;
7. selPress: default to 1.2;
8. elitism: default to 5;
9. relTol: default to 0.1;
10. verbose: default to FALSE (default to true in the functions used by CNORwrap but CNORwrap sets them to false by default).

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)

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".

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.

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)