makeSimModel {INSPEcT} | R Documentation

## Build the synthetic rates shaped on a dataset

### Description

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,
      probs = rbind(synthesis = c(constant = 0.5, sigmoid = 0.3, impulse = 0.2), processing
        = c(constant = 0.5, sigmoid = 0.3, impulse = 0.2), degradation = 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 matrix wich describes the probability of each rate (rows) to be constant, shaped like a sigmoid or like an impulse model (columns)
`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

    nascentInspObj <- readRDS(system.file(package='INSPEcT', 'nascentInspObj.rds'))
    simRates<-makeSimModel(nascentInspObj, 1000, seed=1)
    table(geneClass(simRates))

[Package INSPEcT version 1.20.0 Index]