makeSimDataset: Generate synthetic rates and concentrations

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

Description

This method generates rates and concentrations where noise is added according to the desired number of replicates that the user set as an arguments from the INSPEcT_model object that has been created by the method of the class INSPEcT makeSimModel. Rates and concentrations can be generated at the time-points of interest within the original time window. This method generates an INSPEcT object that can be modeled and the performance of the modeling can be tested directly aginst the INSPEcT_model object created by makeSimModel.

Usage

makeSimDataset(
  object,
  tpts,
  nRep,
  NoNascent = FALSE,
  seed = NULL,
  b = 0.3,
  tL = 1/6,
  noise_sd = 4
)

## S4 method for signature 'INSPEcT_model'
makeSimDataset(
  object,
  tpts,
  nRep,
  NoNascent = FALSE,
  seed = NULL,
  b = 0.3,
  tL = 1/6,
  noise_sd = 4
)

Arguments

object	An object of class INSPEcT_model, usually the output of makeSimModel
tpts	A numeric vector of time points where rates and concentrations have to be evaluated
nRep	Number of replicates to simulate
NoNascent	A logical which, if true, makes the output of the method suitable for an analysis without Nascent. (default=FALSE)
seed	A numeric to obtain reproducible results. When NULL (default) no seed is set.
b	A numeric which represents the probability of contamination of the unlabeled sample due to the labled one
tL	A numeric which represents the labeling time for an ideal nascent RNA profiling, it is required for the contamination analysis. (default=1/6)
noise_sd	A numeric which represents the noise standard deviation. (default=4)

Value

An object of the class ExpressionSet containing rates and concentrations

See Also

makeSimModel

Examples

if( Sys.info()["sysname"] != "Windows" ) {
  nascentInspObj <- readRDS(system.file(package='INSPEcT', 'nascentInspObj.rds'))
  simRates<-makeSimModel(nascentInspObj, 1000, seed=1)
  tpts <- tpts(nascentInspObj)
  nascentSim2replicates <- makeSimDataset(object=simRates,tpts=tpts,nRep=3,NoNascent=FALSE,seed=1)
}

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