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

## Documentation for package ‘INSPEcT’ version 1.4.0

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

## Help Pages

A C D E F G I L M N P R S T U 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

## -- C --

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 two objects of class INSPEcT
compareSteady-method | Generate an object of class INSPEcT_diffsteady from two objects 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 | Gene Names Associated with an Object of Class INSPEcT
featureNames<--method | Gene Names Associated with an Object of Class INSPEcT

## -- 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_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
llrtests | Get or set parameters for model test and selection
llrtests-method | Get or set parameters for model test and selection
llrtests<- | Get or set parameters for model test and selection
llrtests<--method | Get or set parameters for model test and selection
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
makeRPKMs | Calculate RPKM and count values on introns and exons from bam/sam files
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
mycerIds10 | An INSPEcT object with evaluated and modeled rates and concentrations

## -- 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

## -- 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
rpkms | intron, exons RPKM values of 500 genes from 4sU-seq and RNA-seq experiments

## -- S --

sfPlot | A nice plot to see scaling factors used for RNA-seq and 4sU-seq libraries
sfPlot-method | A nice plot to see scaling factors used for RNA-seq and 4sU-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
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
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 --

testingParams | Get or set parameters for model test and selection
thresholds | Get or set parameters for model test and selection
thresholds-method | Get or set parameters for model test and selection
thresholds<- | Get or set parameters for model test and selection
thresholds<--method | Get or set parameters for model test and selection
totalSF | Accessor to the slot totalSF of an INSPEcT object
totalSF-method | Accessor to the slot totalSF of an INSPEcT object
tpts | Accessor to the slot tpts of an INSPEcT object
tpts-method | Accessor to the slot tpts of an INSPEcT object

## -- U --

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

## -- 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