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