modelingParams: Get and set number parameters for the modeling

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

Description

A method to get the parameters used for modeling rates and concentrations by the method modelRates

Usage

modelingParams(object)

## S4 method for signature 'INSPEcT'
modelingParams(object)

Arguments

object

An object of class INSPEcT

Value

List of parameters and their values

• 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.

• useSigmoidFun A logical, whether to choose between sigmoid and impulse function to fit rates and concentrations. In case not, always impulse function is used.

• testOnSmooth A logical, wheter models should be tested on smoothed pre-mRNA, total mRNA and eventually synthesis rates or not.

• nInit number of optimization to find the best functional representation of each rate

• nIter number of max iteration during optimization

• Dmin lower bondary for degradation rates in the NoNascent mode

• Dmax upper bondary for degradation rates in the NoNascent mode

• seed A numeric, indicatindg the seed set for reproducible results.

See Also

modelRates

Examples

nascentInspObj10 <- readRDS(system.file(package='INSPEcT', 'nascentInspObj10.rds'))
modelingParams(nascentInspObj10)

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