AIC-INSPEcT-method      Akaike information criterion calculated for the
                        models evaluated by INSPEcT
Extract                 Extract Parts of an INSPEcT or an INSPEcT_model
                        Object
INSPEcT                 INSPEcT package
INSPEcT-class           An S4 class to contain all rates and models
                        generated by INSPEcT
INSPEcT_diffsteady-class
                        An S4 class to represent comparisons between
                        two steady-state conditions
INSPEcT_model-class     An S4 class to represent models generated by
                        INSPEcT
UCSC_mm9_genes_exons    A Gtf file containing exons definition of 100
                        genes
UCSC_mm9_genes_introns
                        A Gtf file containing introns definition of 100
                        genes
chisqmodel              Retrieve results of chi-squared test for the
                        selected models
chisqtest               Retrieve all results of chi-squared test
combine                 Combine different Objects of Class INSPEcT
compareSteady           Generate an object of class INSPEcT_diffsteady
                        from two objects of class INSPEcT
dim,INSPEcT-method      Dimensions of an Object of Class INSPEcT
featureNames,INSPEcT-method
                        Gene Names Associated with an Object of Class
                        INSPEcT
geneClass               Retrieve the regulatory class for each gene
getModel                Get or replace INSPEcT_model object within
                        INSPEcT object
inHeatmap               Heatmap that represent the fold changes of all
                        the five features
labeledSF               Accessor to the slot labeledSF of an INSPEcT
                        object
logLik                  Retrieve results of log likelihood test
makeModelRates          Calculate modeled rates and concentrations
makeRPKMs               Calculate RPKM and count values on introns and
                        exons from bam/sam files
makeSimDataset          Generate synthetic rates and concentrations
makeSimModel            Build the synthetic rates shaped on a dataset
modelRates              Launch the modeling process
modelSelection          Get or set parameters for model test and
                        selection
modelingParams          Get and set number parameters for the modeling
mycerIds10              An INSPEcT object with evaluated and modeled
                        rates and concentrations
nGenes                  Get the number of genes within the INSPEcT
                        object
nTpts                   Get the number of time points within the
                        INSPEcT object
newINSPEcT              Create a new INSPEcT object
plotGene                Plot the pre-modeled and modeled profiles for
                        one gene
plotMA                  MA-plot from base means and log fold changes
ratePvals               Retrieve a single p-value for each rate
ratesFirstGuess         Retrieve pre-modeling rates and concentrations
ratesFirstGuessVar      Retrieve pre-modeling rates and concentrations
                        variance
removeModel             remove modelling information from INSPEcT
                        object
rocCurve                Display rate classification performance
rocThresholds           Display rate classification performance with
                        thresholds visible at x-axis
rpkms                   intron, exons RPKM values of 500 genes from
                        4sU-seq and RNA-seq experiments
sfPlot                  A nice plot to see scaling factors used for
                        RNA-seq and 4sU-seq libraries
simData1rep             An INSPEcT object with 1000 simulated rates and
                        concentration and their modeled rates
simData3rep             An INSPEcT object with 1000 simulated rates and
                        concentration and their modeled rates
simRates                An INSPEcT_model object of 1000 simulated rates
split                   Divide an INSPEcT Object into groups
totalSF                 Accessor to the slot totalSF of an INSPEcT
                        object
tpts                    Accessor to the slot tpts of an INSPEcT object
viewModelRates          Retrieve the modeled rates and concentrations
