makeSimDataset {INSPEcT} | R Documentation

## Generate synthetic rates and concentrations

### Description

Generate synthetic rates and concentrations

This method generates rates and concentrations where noise is added according to the desired number of replicates that the user set as an arguments from the INSPEcT_model object that has been created by the method of the class INSPEcT `makeSimModel`. Rates and concentrations can be generated at the time-points of interest. This method generates an INSPEcT object that can be modeled and the performance of the modeling can be tested directly aginst the INSPEcT_model object created by `makeSimModel`.

### Usage

    makeSimDataset(object, tpts, nRep, seed = NULL)

    ## S4 method for signature 'INSPEcT_model'
    makeSimDataset(object, tpts, nRep, seed = NULL)

### Arguments

`object` | An object of class INSPEcT_model, usually the output of `makeSimModel`
`tpts` | A numeric vector of time points where rates and concentrations have to be evaluated
`nRep` | Number of replicates to simulate
`seed` | A numeric to obtain reproducible results

### Value

An object of the class ExpressionSet containing rates and concentrations

### See Also

`makeSimModel`

### Examples

    ## generate a synthtic data-set of 10 genes based on the real data-set
    data('rpkms', package='INSPEcT')
    tpts <- c(0, 1/6, 1/3, 1/2, 1, 2, 4, 8, 16)
    tL <- 1/6
    mycerIds <- newINSPEcT(tpts, tL, rpkms$foursu_exons, rpkms$total_exons,
    	rpkms$foursu_introns, rpkms$total_introns, BPPARAM=SerialParam())
    simRates <- makeSimModel(mycerIds, 10)
    simData <- makeSimDataset(simRates, tpts, 1)
    ## load simulated datasets
    data('simRates', package='INSPEcT')
    data('simData3rep', package='INSPEcT')
    ## measure sensitivity/sensibility of synthesis, degradation and processing
    ## rates identification
    dev.new()
    rocCurve(simRates, simData3rep)
    ## measure classification with a different threshold for the chi-squared
    ## test acceptance of models
    rocCurve(simRates, simData3rep, cTsh=.2)

[Package INSPEcT version 1.10.0 Index]