makeOscillatorySimModel: Build the synthetic rates with oscillatory pattern

Description Usage Arguments Value See Also Examples

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
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

1
2
3
nascentInspObj <- readRDS(system.file(package='INSPEcT', 'nascentInspObj.rds'))
simRates<-makeOscillatorySimModel(nascentInspObj, 1000, seed=1)
table(geneClass(simRates))

INSPEcT documentation built on April 29, 2020, 5:19 a.m.