makeSimModel: Build the synthetic rates shaped on a dataset

Description Usage Arguments Details Value See Also Examples

Description

Build the synthetic rates shaped on a dataset

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.

Usage

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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 = c(constant = 0.5,
  sigmoid = 0.3, impulse = 0.2), na.rm = TRUE, seed = NULL)

Arguments

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 vector wich describes the probability of a rate to be constant, shaped like a sigmoid or like an impulse model

na.rm

A logical that set whether missing values in the real dataset should be removed

seed

A numeric to obtain reproducible results

Details

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.

Value

An object of class INSPEcT_model with synthetic rates

See Also

makeSimDataset

Examples

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data('nascentInspObj', package='INSPEcT')
simRates<-makeSimModel(nascentInspObj, 1000, seed=1)
tpts <- simRates@params$tpts

simData2rep_Nascent <- makeSimDataset(object=simRates,tpts=tpts,nRep=3,NoNascent=FALSE,seed=1)
simData2rep_Nascent <- modelRates(simData2rep_Nascent[1:10], seed=1)

ste-depo/INSPEcT documentation built on July 30, 2018, 12:04 p.m.