A C D E F G I L M N P R S T U 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 |
| 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 |
| 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 | Gene Names Associated with an Object of Class INSPEcT |
| featureNames<--method | Gene Names Associated with an Object of Class INSPEcT |
| 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_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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |