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A C D E F G I L M N P Q R S T V misc
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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. |
| 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 |
| 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 |
| tpts | Accessor to the slot tpts of an INSPEcT object |
| tpts-method | Accessor to the slot tpts of an INSPEcT object |
| 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 |
| [-method | Extract Parts of an INSPEcT or an INSPEcT_model Object |
| [-method | An S4 class to represent steady-state analysis without nascent RNA |