CNORwrap {CellNOptR} | R Documentation |
This function is a wrapper around the whole CNOR analysis, it performs the following steps:
Plot the CNOlist;
Checks data to model compatibility;
Call the preprocessing function (Cut the nonc off the model, compress the model and expand the gates);
Compute the residual error;
Prepare for simulation;
Optimisation T1 and T2 (optional);
Plot simulated and experimental results;
Plot the evolution of fit;
Write the scaffold and PKN;
Write the report
CNORwrap(paramsList=NA, data=NA, model=NA, name, namesData=NA, time=1, compression=TRUE, expansion=TRUE, cutNONC=TRUE)
paramsList |
A list of parameters related to the Genetic Algorithm parameters:
|
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) |
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.
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".
C. Terfve
#version with paramslist 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)