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-shinyApps       Run shiny applications contained in the package
                        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
INSPEcT_steadyNoNascent-class
                        An S4 class to represent steady-state analysis
                        without nascent RNA
PTratio                 Calculate post-transcriptional ratio from an
                        object of class INSPEcT_diffsteady
PTreg                   Calculate the post-transcriptional ratio from
                        an object of class INSPEcT_diffsteady
allcounts               A list containing mature and nascent counts for
                        exons and introns, three replicates and 11 time
                        points: 0,1/6,1/3,1/2,1,1.5,2,4,8,12,16 hours.
calculateRatePvals      Calculate a single p-value for each rate
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 an object of class INSPEcT
compareSteadyNoNascent
                        Identify post-transcriptionally regulated genes
                        from an object of class INSPEcT_diffsteady
computeConfidenceIntervals
                        Compute confidence intervals
convergence             Retrieve the convergence for the selected
                        models of each gene
correlationPlot         Display rate classification performance
dim,INSPEcT-method      Dimensions of an Object of Class INSPEcT
featureNames,INSPEcT-method
                        Gene Names Associated with an Object of Class
                        INSPEcT
featureWidths           Contains two variables: "exWdths" and
                        "intWdths" containing the lenght of the exons
                        and introns, respectively, relative to the
                        genes in "allcounts"
geneClass               Retrieve the regulatory class for each gene
inHeatmap               Heatmap that represent the fold changes of all
                        the five features
inspectFromBAM          Wrapper function from BAM files
inspectFromPCR          Wrapper function from PCR quantifications
labeledSF               Accessor to the slot labeledSF of an INSPEcT
                        object
libsizes                Contains two variables: "nascentLS" and
                        "totalLS" containing the sequencing depth of
                        nascent and total libraries respectively,
                        relative to the experiments in "allcounts"
logLik                  Retrieve results of log likelihood test
makeModelRates          Calculate modeled rates and concentrations
makeOscillatorySimModel
                        Build the synthetic rates with oscillatory
                        pattern
makeSimDataset          Generate synthetic rates and concentrations
makeSimModel            Build the synthetic rates shaped on a dataset
mature                  Get mature RNA expressions from an object of
                        class INSPEcT_diffsteady
matureVar               Get mature RNA expressions variances from an
                        object of class INSPEcT_diffsteady
modelRates              Launch the modeling process
modelRatesNF            Launch the modeling process without imposing
                        sigmoid/impulse functional form
modelSelection          Visualize criteria used for rate variability
modelingParams          Get and set number parameters for the modeling
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
plotPMgene              Plot the premature/mature expression of a gene
                        and the global trend from an object of class
                        INSPEcT_diffsteady
plotPMtrend             Plot the premature/mature trend from an object
                        of class INSPEcT_diffsteady
premature               Get premature RNA expressions from an object of
                        class INSPEcT_diffsteady
prematureVar            Get premature RNA expressions variances from an
                        object of class INSPEcT_diffsteady
processingDelay         Classify genes as delayed by the processing
                        using the delta and tau metrics
quantifyExpressionsFromBAMs
                        Evaluate introns and exons expressions from BAM
                        or SAM files
quantifyExpressionsFromBWs
                        Evaluate introns and exons expressions from BAM
                        or SAM files
quantifyExpressionsFromTrAbundance
                        Given introns and exons abundances (for example
                        RPKMs) this method returns their variances
                        evaluated thorugh plgem.
quantifyExpressionsFromTrCounts
                        Evaluates introns and exons RPKMs, per gene,
                        from counts data.
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
setConfidenceIntervals
                        Set confidence intervals
simData3rep_Nascent     An INSPEcT object with 1000 simulated rates and
                        concentration and their modeled rates
simData3rep_NoNascent   An INSPEcT object with 1000 simulated rates and
                        concentration and their modeled rates
simData4rep_Nascent     An INSPEcT object with 1000 simulated rates and
                        concentration and their modeled rates
simData4rep_NoNascent   An INSPEcT object with 1000 simulated rates and
                        concentration and their modeled rates
split                   Divide an INSPEcT Object into groups
tpts                    Accessor to the slot tpts of an INSPEcT object
viewConfidenceIntervals
                        Retrieve the modeled Confidence Intervals
viewModelRates          Retrieve the modeled rates and concentrations
