INSPEcT-class: An S4 class to contain all rates and models generated by...
In INSPEcT: Modeling RNA synthesis, processing and degradation with RNA-seq data

Description Usage Arguments Details Value Slots

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 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.

1 2	## S4 method for signature 'INSPEcT' show(object)

object

An object of class INSPEcT

Methods that apply to INSPEcT class are AIC
[
calculateDelta
calculateRatePvals
calculateTau
chisqmodel
chisqtest
combine
compareSteady
compareSteadyNoNascent
computeConfidenceIntervals
correlationPlot
dim
featureNames
geneClass
inHeatmap
labeledSF
logLik
makeModelRates
makeOscillatorySimModel
makeSimModel
modelRates
modelRatesNF
modelSelection
modelingParams
nGenes
nTpts
plotGene
processingDelay
ratePvals
ratesFirstGuess
ratesFirstGuessVar
removeModel
rocCurve
rocThresholds
setConfidenceIntervals
show
split
tpts
viewConfidenceIntervals
viewModelRates

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

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)
ratesFirstGuessVar: An object of class ExpressionSet that contains the variances related to rates and concentrations guessed from the first part of INSPEcT analysis (before modeling)
confidenceIntervals: An object of class ExpressionSet that contains the confidence intervals.
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.
ratePvals: A matrix containing the p-value relative to the variability of synthesis, processing and degradation for each gene.
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.
tL: A numeric containing the length of the Nascent pulse.
NoNascent: A logical indicating if the nascent RNA was included into the analysis.
NF: A logical indicating if the modeling approach is Non-Functional
degDuringPulse: A logical indicating if degradation of RNA during the 4sU pulse was considered.
version: A character indicating the version of INSPEcT that created the object