makeSimModel {INSPEcT} | R Documentation

## Build the synthetic rates shaped on a dataset

### Description

Build the synthetic rates shaped on a dataset

This method allow the creation of synthesis, degradation and processing rates for a certain number of genes. The rates are created according to the distributions of the real data-set which is given as an input of the method. Different proportions of constant varying rates can be set and a new vector of time points can be provided. This method has to be used before the `makeSimDataset` method.

### Usage

    makeSimModel(object, nGenes, newTpts = NULL, probs = c(constant = 0.5,
      sigmoid = 0.3, impulse = 0.2), na.rm = TRUE, seed = NULL)

    ## S4 method for signature 'INSPEcT'
    makeSimModel(object, nGenes, newTpts = NULL,
      probs = c(constant = 0.5, sigmoid = 0.3, impulse = 0.2), na.rm = TRUE,
      seed = NULL)

### Arguments

`object` | An object of class INSPEcT
`nGenes` | A numeric with the number of synthtic genes to be created
`newTpts` | A numeric verctor with time points of the synthtic dataset, if NULL the time points of the real dataset will be used
`probs` | A numeric vector wich describes the probability of a rate to be constant, shaped like a sigmoid or like an impulse model
`na.rm` | A logical that set whether missing values in the real dataset should be removed
`seed` | A numeric to obtain reproducible results

### Details

The method `makeSimModel` generates an object of class INSPEcT_model that stores the parametric functions to genrate clean rates of a time-course. To any of the rates also a noise variance is associate but not used yet. In a typical workflow the output of `makeSimModel` is the input of the method `makeSimDataset`, that build the noisy rates and concentrations, given a specified number of replicates.

### Value

An object of class INSPEcT_model with synthetic rates

### See Also

`makeSimDataset`

### Examples

    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())
    ## generate a synthtic data-set of 10 genes based on the real data-set
    simRates <- makeSimModel(mycerIds, 10)
    simData <- makeSimDataset(simRates, tpts, 1)
    ## measure sensitivity/sensibility of synthesis, degradation and processing
    ## rates identification
    data('simRates', package='INSPEcT')
    data('simData3rep', package='INSPEcT')
    rocCurve(simRates, simData3rep)
    ## measure classification with a different threshold for the chi-suared
    ## test acceptance of models
    rocCurve(simRates, simData3rep, cTsh=.2)
    ## generate a synthtic data-set of 10 genes based on the real data-set
    ## with more replicates and more time points
    ## Not run:
    newTpts <- c(0, 1/6, 1/3, 1/2, 1, 1.5, 2, 4, 8, 12, 16, 24)
    simRates <- makeSimModel(mycerIds, 10, newTpts=newTpts)
    simData <- makeSimDataset(simRates, newTpts, 3)

    ## End(Not run)

[Package INSPEcT version 1.10.0 Index]