Extract
(Package: INSPEcT) :
Extract Parts of an INSPEcT or an INSPEcT_model Object
Operators acting on INSPEcT or INSPEcT_model objects to extract parts. INSPEcT_model objects can be subsetted only by gene. INSPEcT objects can be subsetted either by gene id or time point. In case of subsetting an INSPEcT object by time point, the model should be empty.
INSPEcT-class
(Package: INSPEcT) :
An S4 class to contain all rates and models generated by INSPEcT
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.
INSPEcT (INference of Synthesis, Processing and dEgradation rates in Time-cousre experiments) is a package that analyse 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and asses via modeling the rates that determines changes in mature mRNA levels.
INSPEcT_diffsteady is a class able to store the results of the comparisons between two steady states. An object of class INSPEcT_diffsteady is created with the method "compareSteady" applied on two "INSPEcT" objects (see compareSteady).
INSPEcT_model is a class able to store all the results of the modeling of synthesis, processing and degradation rates made via the method modelRates (slot ratesSpecs). It also stores the criteria (slot parameter) to choose between the many models tested for each gene the one that better describes the data and the results. The slot simple is a flag that distinguish wheter the model contains the information of the introns or not. In case not, the flag simple is set to TRUE. Also the method makeSimModel of class INSPEcT-class creates an object of class INSPEcT_model. This object will be used by makeSimDataset to generate a complete simulated data-set, whose classification performance can be tested.
providing 
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