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 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
.
## 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
llrtests
logLik
makeModelRates
makeSimModel
modelingParams<-
modelingParams
modelRates
modelSelection
nGenes
nTpts
plotGene
ratePvals
ratesFirstGuessVar
ratesFirstGuess
removeModel
sfPlot
thresholds
totalSF
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)
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