modelRates: Launch the modeling process

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

Description

Launch the modeling process with parameters set with modelingParams

This method model the synthesis, degradation and processing rates after their estimation by the constructor function newINSPEcT. Estimated rates are not guaranteed to optimally describes provided input data yet. To this purpose, modeled rates can be generated and genes can be assigned to a transcriptional regulatory mechanism. Modeled rates can be accessed via the method viewModelRates and gene classification according to the regulatory mechanism can be accessed by geneClass. The modeling options used for the modeling can be later accessed by the user via modelingParams. After modeling, model selection is run by the method calculateRatePvals with default parameters.

Usage

modelRates(
  object,
  estimateRatesWith = c("der", "int"),
  useSigmoidFun = TRUE,
  nInit = 10,
  nIter = 300,
  Dmin = 1e-06,
  Dmax = 10,
  seed = NULL,
  BPPARAM = SerialParam()
)

## S4 method for signature 'INSPEcT'
modelRates(
  object,
  estimateRatesWith = c("der", "int"),
  useSigmoidFun = TRUE,
  nInit = 10,
  nIter = 300,
  Dmin = 1e-06,
  Dmax = 10,
  seed = NULL,
  BPPARAM = SerialParam()
)

Arguments

object	An object of class INSPEcT
estimateRatesWith	Either "int" or "der". With "int" the degradation and processing rates are estimated integrating the system between one time point and the following. With "der" degradation and processing rates are estimated using the derivative of total and pre mRNA. (default is "der")
useSigmoidFun	A logical, whether to choose between sigmoid and impulse function to fit rates and concentrations. In case not, always impulse function is used. (default is TRUE)
nInit	number of optimization to find the best functional representation of each rate (by default 10)
nIter	number of max iteration during optimization (default is 300)
Dmin	lower bondary for degradation rates in the NoNascent mode (default 1e-06)
Dmax	upper bondary for degradation rates in the NoNascent mode (default 10)
seed	A numeric, indicatindg the seed to be set for reproducible results. If NULL it is randomly selected (default NULL)
BPPARAM	Parallelization parameters for bplapply. By default SerialParam()

Value

An object of class INSPEcT with modeled rates

See Also

viewModelRates, calculateRatePvals, geneClass

Examples

if( Sys.info()["sysname"] != "Windows" ) {
	nascentInspObj10 <- readRDS(system.file(package='INSPEcT', 'nascentInspObj10.rds'))
	## models removal
	nascentInspObjThreeGenes <- removeModel(nascentInspObj10[1:3])
	nascentInspObjThreeGenes <- modelRates(nascentInspObjThreeGenes, 
	  seed=1, BPPARAM=SerialParam())
	## view modeled synthesis rates
	viewModelRates(nascentInspObjThreeGenes, 'synthesis')
	## view gene classes
	geneClass(nascentInspObjThreeGenes)
}

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