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