modelingParams {INSPEcT} | R Documentation

## Get and set number parameters for the modeling

### Description

A method to get and set the parameters that will be used in the modeling of estimated rates and concentrations by the method `modelRates`

### Usage

    modelingParams(object)

    modelingParams(object) <- value

    ## S4 method for signature 'INSPEcT'
    modelingParams(object)

    ## S4 replacement method for signature 'INSPEcT'
    modelingParams(object) <- value

### Arguments

`object` | An object of class INSPEcT
`value` | A list with new parameters

### Value

List of parameters and their values

- nInit number of optimization to find the best functional representation of each rate (by default 10)

- nIter number of max iteration during optimization (default is 300)

- na.rm A logical wheter missing values should be removed from estimated rates (default is TRUE)

- verbose A logical wheter to be verbose or not (default is TRUE)

- estimateRatesWith Either "int" or "der". With "int" the degradation and processing rates are estimated integrating the system between one time point and the following. With "der" degradation and processing rates are estimated using the derivative of total and pre mRNA. (default is "int")

- useSigmoidFun A logical, whether to choose between sigmoid and impulse function to fit rates and concentrations. In case not, always impulse function is used. (default is TRUE)

- testOnSmooth A logical, wheter models should be tested on smoothed pre-mRNA, total mRNA and eventually synthesis rates or not. (default is TRUE)

### See Also

`modelRates`

### Examples

    nascentInspObj10 <- readRDS(system.file(package='INSPEcT', 'nascentInspObj10.rds'))
    modelingParams(nascentInspObj10)
    nascentInspObj10 <- readRDS(system.file(package='INSPEcT', 'nascentInspObj10.rds'))
    nascentInspObj10 <- removeModel(nascentInspObj10)
    modelingParams(nascentInspObj10)$useSigmoidFun <- FALSE

[Package INSPEcT version 1.12.2 Index]