modelRates {INSPEcT} | R Documentation

## Launch the modeling process

### Description

Launch the modeling process with parameters set with `modelingParams`

This method model the synthesis, degradation and processing rates after their estimation by the constructor function `newINSPEcT`. Estimated rates are not guaranteed to optimally describes provided input data yet. To this purpose, modeled rates can be generated and genes can be assigned to a transcriptional regulatory mechanism. Modeled rates can be accessed via the method `viewModelRates` and gene classification according to the regulatory mechanism can be accessed by `geneClass`. The modeling options used for the modeling can be later accessed by the user via `modelingParams`. After modeling, model selection is run by the method `calculateRatePvals` with default parameters.

### Usage

    modelRates(
      object,
      estimateRatesWith = c("der", "int"),
      useSigmoidFun = TRUE,
      nInit = 10,
      nIter = 300,
      Dmin = 1e-06,
      Dmax = 10,
      seed = NULL,
      BPPARAM = SerialParam()
    )

    ## S4 method for signature 'INSPEcT'
    modelRates(
      object,
      estimateRatesWith = c("der", "int"),
      useSigmoidFun = TRUE,
      nInit = 10,
      nIter = 300,
      Dmin = 1e-06,
      Dmax = 10,
      seed = NULL,
      BPPARAM = SerialParam()
    )

### Arguments

`object` | An object of class INSPEcT
`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 "der")
`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)
`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)
`Dmin` | lower bondary for degradation rates in the NoNascent mode (default 1e-06)
`Dmax` | upper bondary for degradation rates in the NoNascent mode (default 10)
`seed` | A numeric, indicatindg the seed to be set for reproducible results. If NULL it is randomly selected (default NULL)
`BPPARAM` | Parallelization parameters for bplapply. By default SerialParam()

### Value

An object of class INSPEcT with modeled rates

### See Also

`viewModelRates`, `calculateRatePvals`, `geneClass`

### Examples

    if( Sys.info()["sysname"] != "Windows" ) {
    	nascentInspObj10 <- readRDS(system.file(package='INSPEcT', 'nascentInspObj10.rds'))
    	## models removal
    	nascentInspObjThreeGenes <- removeModel(nascentInspObj10[1:3])
    	nascentInspObjThreeGenes <- modelRates(nascentInspObjThreeGenes,
    	  seed=1, BPPARAM=SerialParam())
    	## view modeled synthesis rates
    	viewModelRates(nascentInspObjThreeGenes, 'synthesis')
    	## view gene classes
    	geneClass(nascentInspObjThreeGenes)
    }

[Package INSPEcT version 1.20.0 Index]