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

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 collected (slot tpts), the labeling time (slot tL) and the normalization scale fators used for RNA- (totalSF) and 4sU-seq libraries (labeledSF). 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

"show"(object)

Arguments

object

An object of class INSPEcT

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)
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 4sU-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 4sU pulse

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