makeOscillatorySimModel: Build the synthetic rates with oscillatory pattern

In INSPEcT: Modeling RNA synthesis, processing and degradation with RNA-seq data

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))

INSPEcT documentation built on Nov. 8, 2020, 6:49 p.m.