Man pages for ste-depo/INSPEcT
Modeling RNA synthesis, processing and degradation with RNA-seq data
| AIC-INSPEcT-method | Akaike information criterion calculated for the models... |
| allcounts | A list containing mature and nascent counts for exons and... |
| calculateRatePvals | Calculate a single p-value for each rate |
| chisqmodel | Retrieve results of chi-squared test for the selected models |
| chisqtest | Retrieve all results of chi-squared test |
| combine | Combine different Objects of Class INSPEcT |
| compareSteady | Generate an object of class INSPEcT_diffsteady from an object... |
| compareSteadyNoNascent | Identify post-transcriptionally regulated genes from an... |
| computeConfidenceIntervals | Compute confidence intervals |
| convergence | Retrieve the convergence for the selected models of each gene |
| correlationPlot | Display rate classification performance |
| dim-INSPEcT-method | Dimensions of an Object of Class INSPEcT |
| Extract | Extract Parts of an INSPEcT or an INSPEcT_model Object |
| featureNames-INSPEcT-method | Gene Names Associated with an Object of Class INSPEcT |
| featureWidths | Contains two variables: "exWdths" and "intWdths" containing... |
| geneClass | Retrieve the regulatory class for each gene |
| inHeatmap | Heatmap that represent the fold changes of all the five... |
| INSPEcT | INSPEcT package |
| INSPEcT-class | An S4 class to contain all rates and models generated by... |
| INSPEcT_diffsteady-class | An S4 class to represent comparisons between two steady-state... |
| inspectFromBAM | Wrapper function from BAM files |
| inspectFromPCR | Wrapper function from PCR quantifications |
| INSPEcT_model-class | An S4 class to represent models generated by INSPEcT |
| INSPEcT-shinyApps | Run shiny applications contained in the package INSPEcT |
| INSPEcT_steadyNoNascent-class | An S4 class to represent steady-state analysis without... |
| labeledSF | Accessor to the slot labeledSF of an INSPEcT object |
| libsizes | Contains two variables: "nascentLS" and "totalLS" containing... |
| logLik | Retrieve results of log likelihood test |
| makeModelRates | Calculate modeled rates and concentrations |
| makeOscillatorySimModel | Build the synthetic rates with oscillatory pattern |
| makeSimDataset | Generate synthetic rates and concentrations |
| makeSimModel | Build the synthetic rates shaped on a dataset |
| mature | Get mature RNA expressions from an object of class... |
| matureVar | Get mature RNA expressions variances from an object of class... |
| modelingParams | Get and set number parameters for the modeling |
| modelRates | Launch the modeling process |
| modelRatesNF | Launch the modeling process without imposing sigmoid/impulse... |
| modelSelection | Visualize criteria used for rate variability |
| newINSPEcT | Create a new INSPEcT object |
| nGenes | Get the number of genes within the INSPEcT object |
| nTpts | Get the number of time points within the INSPEcT object |
| plotGene | Plot the pre-modeled and modeled profiles for one gene |
| plotMA | MA-plot from base means and log fold changes |
| plotPMgene | Plot the premature/mature expression of a gene and the global... |
| plotPMtrend | Plot the premature/mature trend from an object of class... |
| premature | Get premature RNA expressions from an object of class... |
| prematureVar | Get premature RNA expressions variances from an object of... |
| processingDelay | Classify genes as delayed by the processing using the delta... |
| PTratio | Calculate post-transcriptional ratio from an object of class... |
| PTreg | Calculate the post-transcriptional ratio from an object of... |
| 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... |
| quantifyExpressionsFromTrCounts | Evaluates introns and exons RPKMs, per gene, from counts... |
| ratePvals | Retrieve a single p-value for each rate |
| ratesFirstGuess | Retrieve pre-modeling rates and concentrations |
| ratesFirstGuessVar | Retrieve pre-modeling rates and concentrations variance |
| removeModel | remove modelling information from INSPEcT object |
| rocCurve | Display rate classification performance |
| rocThresholds | Display rate classification performance with thresholds... |
| setConfidenceIntervals | Set confidence intervals |
| simData3rep_Nascent | An INSPEcT object with 1000 simulated rates and concentration... |
| simData3rep_NoNascent | An INSPEcT object with 1000 simulated rates and concentration... |
| simData4rep_Nascent | An INSPEcT object with 1000 simulated rates and concentration... |
| simData4rep_NoNascent | An INSPEcT object with 1000 simulated rates and concentration... |
| split | Divide an INSPEcT Object into groups |
| tpts | Accessor to the slot tpts of an INSPEcT object |
| viewConfidenceIntervals | Retrieve the modeled Confidence Intervals |
| viewModelRates | Retrieve the modeled rates and concentrations |
