makeSimModel: Build the synthetic rates shaped on a dataset

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

Description

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

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
)

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 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

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

nascentInspObj <- readRDS(system.file(package='INSPEcT', 'nascentInspObj.rds'))
simRates<-makeSimModel(nascentInspObj, 1000, seed=1)
table(geneClass(simRates))

ste-depo/INSPEcT documentation built on Oct. 3, 2020, 9:14 p.m.