INSPEcT-class: An S4 class to contain all rates and models generated by...

Description Usage Arguments Details Value Slots

Description

INSPEcT is a class able to store all the estimated rates and concentrations (slot ratesFirstGuess), the modeled rates and concentrations (slot modelRates) and the model themselves (slot model). Within the class INSPEcT other information regarding the experimental design are stored, such as the time points where experiments were performed (slot tpts) and, if provided, the nascent RNA collecting time (slot tL) and the normalization scale fators used for mature (totalSF) and nascent (labeledSF) RNA-seq libraries. A list of parameters that will be used during the modeling process is stored within the slot params and can be accessed by modelingParams. A new instance of the class INSPEcT can be generated by the constructor function newINSPEcT.

Usage

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

Arguments

object

An object of class INSPEcT

Details

Methods that apply to INSPEcT class are

[
AIC
chisqmodel
chisqtest
combine
dim
featureNames
geneClass
getModel<-
getModel
inHeatmap
labeledSF llrtests
logLik
makeModelRates
makeSimModel
modelingParams<-
modelingParams
modelRates
modelSelection
nGenes
nTpts
plotGene
ratePvals
ratesFirstGuessVar
ratesFirstGuess
removeModel
sfPlot
thresholds
totalSF
tpts
viewModelRates

Value

Method show for objects of class INSPEcT displays the main features of the slots ratesFirstGuess, model and modelRates

Slots

params

A list of parameters of the modeling part

ratesFirstGuess

An object of class ExpressionSet that contains all the rates and concentrations guessed from the first part of INSPEcT analysis (before modeling)

ratesFirstGuessP

An object containing the rates first guess part of INSPEcT analysis (before modeling)

precision

A matrix that contains the estimated precision of the rates. Rows represent genes, Columns represent time points.

model

An object of class INSPEcT_model that contains the output of the mdoeling

modelRates

An object of class ExpressionSet that contains all modeled the rates and concentrations

tpts

A numeric vector of the time-points

labeledSF

A numeric vector of the scaling factor used for inter time-point normalization of Nascent-seq libraries

totalSF

A numeric vector of the scaling factor used for inter time-point normalization of RNA-seq libraries

tL

A numeric containing the length of the Nascent pulse


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