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 |
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_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 |
makeExonsGtfFromDb | Make a GTF file of exonic or intronic features from a TxDb object |
makeExonsGtfFromDb-method | Make a GTF file of exonic or intronic features from a TxDb object |
makeGtfFromDb | Make a GTF file of exonic or intronic features from a TxDb object |
makeIntronsGtfFromDb | Make a GTF file of exonic or intronic features from a TxDb object |
makeIntronsGtfFromDb-method | Make a GTF file of exonic or intronic features from a TxDb object |
makeModelRates | Calculate modeled rates and concentrations |
makeModelRates-method | Calculate modeled rates and concentrations |
makeRPKMs | Calculate RPKM values on introns and exons from 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 |
nCores | Get and set number of cores to be used for the modeling |
nCores-method | Get and set number of cores to be used for the modeling |
nCores<- | Get and set number of cores to be used for the modeling |
nCores<--method | Get and set number of cores to be used for the modeling |
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 |
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 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 |
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 |