A C D E F G I L M N P Q R S T V misc
INSPEcT-package | INSPEcT package |
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. |
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 |
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 |
Extract | Extract Parts of an INSPEcT or an INSPEcT_model Object |
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" |
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 |
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 |
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 |
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 |
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 |
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 |
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. |
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 |
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 |
tpts | Accessor to the slot tpts of an INSPEcT object |
tpts-method | Accessor to the slot tpts of an INSPEcT object |
viewModelRates | Retrieve the modeled rates and concentrations |
viewModelRates-method | Retrieve the modeled rates and concentrations |
[-method | Extract Parts of an INSPEcT or an INSPEcT_model Object |