makeOscillatorySimModel {INSPEcT} | R Documentation

## Build the synthetic rates with oscillatory pattern

### Description

This method allow the creation of synthesis, degradation and processing rates that generate an oscillatory expression with a period of 24 hours. Two modes are available: one where oscillations arise just by oscillations in the synthesis of the genes (oscillatoryk3=FALSE, default) and another one where both synthesis and degradation rates oscillates (oscillatoryk3=TRUE). In this latter case, the oscillations of the two rates can be coupled by a cetrain delay (parametrer k3delay). After the creation of the synthetic rates, a dataset with noise and contamination added can be made by `makeSimDataset`.

### Usage

    makeOscillatorySimModel(
      object,
      nGenes,
      oscillatoryk3 = FALSE,
      k3delay = NULL,
      na.rm = TRUE,
      seed = NULL
    )

    ## S4 method for signature 'INSPEcT'
    makeOscillatorySimModel(
      object,
      nGenes,
      oscillatoryk3 = FALSE,
      k3delay = NULL,
      na.rm = TRUE,
      seed = NULL
    )

### Arguments

`object` | An object of class INSPEcT
`nGenes` | A numeric with the number of synthtic genes to be created
`oscillatoryk3` | A logical that enables also degradation rate to oscillate
`k3delay` | A numeric that set the delay between synthesis and degradation oscillations. When NULL, no coupling between the two oscillations is set.
`na.rm` | A logical that set whether missing values in the real dataset should be removed
`seed` | A numeric to obtain reproducible results

### Value

An object of class INSPEcT_model with synthetic rates

### See Also

`makeSimModel`

### Examples

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

[Package INSPEcT version 1.20.0 Index]