INSPEcT-class {INSPEcT} | R Documentation |
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
.
## S4 method for signature 'INSPEcT' show(object)
object |
An object of class INSPEcT |
Methods that apply to INSPEcT class are
[
AIC
chisqmodel
chisqtest
combine
dim
featureNames
geneClass
getModel<-
getModel
inHeatmap
labeledSF
logLik
makeModelRates
makeSimModel
modelingParams<-
modelingParams
modelRates
modelSelection
nGenes
nTpts
plotGene
ratePvals
ratesFirstGuessVar
ratesFirstGuess
removeModel
sfPlot
tpts
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)
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.
tL
A numeric containing the length of the Nascent pulse.
NoNascent
A logical indicating if the nascent RNA was included into the analysis.
degDuringPulse
A logical indicating if degradation of RNA during the 4sU pulse was considered.