# Modeling RNA synthesis, processing and degradation with RNA-seq data

## Documentation for package ‘INSPEcT’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G I L M N P Q R S T V misc

## -- A --

AIC-INSPEcT-method | Akaike information criterion calculated for the models evaluated by INSPEcT
AIC-method | Akaike information criterion calculated for the models evaluated by INSPEcT
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.

## -- C --

calculateDelta | Classify genes as delayed by the processing using the delta and tau metrics
calculateDelta-method | Classify genes as delayed by the processing using the delta and tau metrics
calculateRatePvals | Calculate a single p-value for each rate
calculateRatePvals-method | Calculate a single p-value for each rate
calculateTau | Classify genes as delayed by the processing using the delta and tau metrics
calculateTau-method | Classify genes as delayed by the processing using the delta and tau metrics
chisqmodel | Retrieve results of chi-squared test for the selected models
chisqmodel-method | Retrieve results of chi-squared test for the selected models
chisqtest | Retrieve all results of chi-squared test
chisqtest-method | Retrieve all results of chi-squared test
combine | Combine different Objects of Class INSPEcT
combine-method | Combine different Objects of Class INSPEcT
compareSteady | Generate an object of class INSPEcT_diffsteady from an object of class INSPEcT
compareSteady-method | 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
compareSteadyNoNascent-method | Identify post-transcriptionally regulated genes from an object of class INSPEcT_diffsteady
computeConfidenceIntervals | Compute confidence intervals
computeConfidenceIntervals-method | Compute confidence intervals
convergence | Retrieve the convergence for the selected models of each gene
convergence-method | Retrieve the convergence for the selected models of each gene
correlationPlot | Display rate classification performance
correlationPlot-method | Display rate classification performance

## -- D --

degradation | An S4 class to represent comparisons between two steady-state conditions
degradation-method | An S4 class to represent comparisons between two steady-state conditions
dim-method | Dimensions of an Object of Class INSPEcT

## -- E --

Extract | Extract Parts of an INSPEcT or an INSPEcT_model Object

## -- F --

featureNames-method | An S4 class to represent comparisons between two steady-state conditions
featureNames-method | Gene Names Associated with an Object of Class INSPEcT
featureNames<--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"

## -- G --

geneClass | Retrieve the regulatory class for each gene
geneClass-method | Retrieve the regulatory class for each gene

## -- I --

inHeatmap | Heatmap that represent the fold changes of all the five features
inHeatmap-method | Heatmap that represent the fold changes of all the five features
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
inspectFromBAM | Wrapper function from BAM files
inspectFromPCR | Wrapper function from PCR quantifications
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

## -- L --

labeledSF | Accessor to the slot labeledSF of an INSPEcT object
labeledSF-method | 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
logLik-method | Retrieve results of log likelihood test

## -- M --

makeModelRates | Calculate modeled rates and concentrations
makeModelRates-method | Calculate modeled rates and concentrations
makeOscillatorySimModel | Build the synthetic rates with oscillatory pattern
makeOscillatorySimModel-method | Build the synthetic rates with oscillatory pattern
makeSimDataset | Generate synthetic rates and concentrations
makeSimDataset-method | Generate synthetic rates and concentrations
makeSimModel | Build the synthetic rates shaped on a dataset
makeSimModel-method | Build the synthetic rates shaped on a dataset
mature | Get mature RNA expressions from an object of class INSPEcT_diffsteady
mature-method | Get mature RNA expressions from an object of class INSPEcT_diffsteady
matureVar | Get mature RNA expressions variances from an object of class INSPEcT_diffsteady
matureVar-method | Get mature RNA expressions variances from an object of class INSPEcT_diffsteady
modelingParams | Get and set number parameters for the modeling
modelingParams-method | Get and set number parameters for the modeling
modelRates | Launch the modeling process
modelRates-method | Launch the modeling process
modelRatesNF | Launch the modeling process without imposing sigmoid/impulse functional form
modelRatesNF-method | Launch the modeling process without imposing sigmoid/impulse functional form
modelSelection | Visualize criteria used for rate variability
modelSelection-method | Visualize criteria used for rate variability

## -- N --

newINSPEcT | Create a new INSPEcT object
nGenes | Get the number of genes within the INSPEcT object
nGenes-method | Get the number of genes within the INSPEcT object
nTpts | Get the number of time points within the INSPEcT object
nTpts-method | Get the number of time points within the INSPEcT object

## -- P --

plotGene | Plot the pre-modeled and modeled profiles for one gene
plotGene-method | Plot the pre-modeled and modeled profiles for one gene
plotMA | MA-plot from base means and log fold changes
plotMA-method | 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
plotPMgene-method | 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
plotPMtrend-method | Plot the premature/mature trend from an object of class INSPEcT_diffsteady
premature | Get premature RNA expressions from an object of class INSPEcT_diffsteady
premature-method | Get premature RNA expressions from an object of class INSPEcT_diffsteady
prematureVar | Get premature RNA expressions variances from an object of class INSPEcT_diffsteady
prematureVar-method | Get premature RNA expressions variances from an object of class INSPEcT_diffsteady
processing | An S4 class to represent comparisons between two steady-state conditions
processing-method | An S4 class to represent comparisons between two steady-state conditions
processingDelay | Classify genes as delayed by the processing using the delta and tau metrics
processingDelay-method | Classify genes as delayed by the processing using the delta and tau metrics
PTratio | Calculate post-transcriptional ratio from an object of class INSPEcT_diffsteady
PTratio-method | Calculate post-transcriptional ratio from an object of class INSPEcT_diffsteady
PTreg | Calculate the post-transcriptional ratio from an object of class INSPEcT_diffsteady
PTreg-method | Calculate the post-transcriptional ratio from an object of class INSPEcT_diffsteady

## -- Q --

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.

## -- R --

ratePvals | Retrieve a single p-value for each rate
ratePvals-method | Retrieve a single p-value for each rate
ratesFirstGuess | Retrieve pre-modeling rates and concentrations
ratesFirstGuess-method | Retrieve pre-modeling rates and concentrations
ratesFirstGuessVar | Retrieve pre-modeling rates and concentrations variance
ratesFirstGuessVar-method | Retrieve pre-modeling rates and concentrations variance
removeModel | remove modelling information from INSPEcT object
removeModel-method | remove modelling information from INSPEcT object
rocCurve | Display rate classification performance
rocCurve-method | Display rate classification performance
rocThresholds | Display rate classification performance with thresholds visible at x-axis
rocThresholds-method | Display rate classification performance with thresholds visible at x-axis
runINSPEcTGUI | Run shiny applications contained in the package INSPEcT
runProcessingRateDelay | Run shiny applications contained in the package INSPEcT

## -- S --

setConfidenceIntervals | Set confidence intervals
setConfidenceIntervals-method | Set confidence intervals
show-method | An S4 class to contain all rates and models generated by INSPEcT
show-method | An S4 class to represent comparisons between two steady-state conditions
show-method | An S4 class to represent models generated by INSPEcT
show-method | An S4 class to represent steady-state analysis without nascent RNA
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
split-method | Divide an INSPEcT Object into groups
synthesis | An S4 class to represent comparisons between two steady-state conditions
synthesis-method | An S4 class to represent comparisons between two steady-state conditions

## -- T --

tpts | Accessor to the slot tpts of an INSPEcT object
tpts-method | Accessor to the slot tpts of an INSPEcT object

## -- V --

viewConfidenceIntervals | Retrieve the modeled Confidence Intervals
viewConfidenceIntervals-method | Retrieve the modeled Confidence Intervals
viewModelRates | Retrieve the modeled rates and concentrations
viewModelRates-method | Retrieve the modeled rates and concentrations

## -- misc --

[-method | Extract Parts of an INSPEcT or an INSPEcT_model Object
[-method | An S4 class to represent steady-state analysis without nascent RNA