makeOscillatorySimModel {INSPEcT} | R Documentation |
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
.
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 )
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 |
An object of class INSPEcT_model with synthetic rates
nascentInspObj <- readRDS(system.file(package='INSPEcT', 'nascentInspObj.rds')) simRates<-makeOscillatorySimModel(nascentInspObj, 1000, seed=1) table(geneClass(simRates))