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


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Documentation for package ‘INSPEcT’ version 1.0.2

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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