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

Documentation for package ‘INSPEcT’ version 1.39.1

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-- 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