Analysis of 4sU-seq and RNA-seq time-course data

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Documentation for package ‘INSPEcT’ version 1.12.2

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

INSPEcT-package INSPEcT package

-- 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
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 Compare mature RNA steady state data from an object of class INSPEcT
compareSteadyNoNascent-method Compare mature RNA steady state data from an object of class INSPEcT

-- 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
getModel Get or replace INSPEcT_model object within INSPEcT object
getModel-method Get or replace INSPEcT_model object within INSPEcT object
getModel<- Get or replace INSPEcT_model object within INSPEcT object
getModel<--method Get or replace INSPEcT_model object within INSPEcT object

-- 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
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

-- 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
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
modelingParams Get and set number parameters for the modeling
modelingParams-method Get and set number parameters for the modeling
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
modelSelection Get or set parameters for model test and selection
modelSelection-method Get or set parameters for model test and selection
modelSelection<- Get or set parameters for model test and selection
modelSelection<--method Get or set parameters for model test and selection

-- 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
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

-- Q --

quantifyExpressionsFromBAMs 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
runProcessingRateDelay Run shiny applications contained in the package INSPEcT
runRNAdynamics Run shiny applications contained in the package INSPEcT

-- S --

sfPlot A nice plot to see scaling factors used for RNA-seq and Nascent-seq libraries
sfPlot-method A nice plot to see scaling factors used for RNA-seq and Nascent-seq libraries
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
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 --

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