Man pages for TReNA
Fit transcriptional regulatory networks using gene expression, priors, machine learning
| BayesSpikeSolver | Create a Solver class object using the Bayes Spike Solver |
| BayesSpikeSolver-class | An S4 class to represent a Bayes Spike solver |
| CandidateFilter-class | CandidateFilter |
| closeDatabaseConnections | Close a Footprint Database Connection |
| EnsembleSolver | Create a Solver class object using an ensemble of solvers |
| EnsembleSolver-class | Class EnsembleSolver |
| FootprintFilter-class | Create a FootprintFilter object |
| FootprintFinder-class | Class FootprintFinder |
| getAssayData | Retrieve the assay matrix of gene expression data from a... |
| getCandidates | Get candidate genes using a CandidateFilter object |
| getCandidates-FootprintFilter-method | Get candidate genes using the variance filter |
| getCandidates-NullFilter-method | Get candidate genes using the null filter |
| getCandidates-VarianceFilter-method | Get candidate genes using the variance filter |
| getChromLoc | Get Chromasome Location |
| getFilterAssayData | Retrieve the assay matrix of gene expression data |
| getFootprintsForGene | Get Footprints for Gene |
| getFootprintsInRegion | Get Footprints in a Region |
| getGenePromoterRegion | Get Gene Promoter Region |
| getGtfGeneBioTypes | Get the List of Biotypes |
| getGtfMoleculeTypes | Get the List of Molecule Types |
| getPromoterRegionsAllGenes | Get Promoter Regions for All Genes |
| getSolverName | Get the Solver Name from a TReNA Object |
| getSolverObject | Get the Solver Object from a TReNA Object |
| LassoPVSolver | Create a Solver class object using the LASSO P-Value solver |
| LassoPVSolver-class | An S4 class to represent a LASSO P-Value solver |
| LassoSolver | Create a Solver class object using the LASSO solver |
| LassoSolver-class | Class LassoSolver |
| mapMotifsToTFsMergeIntoTable | Map Motifs to Transcription Factors and Merge into a Table |
| NullFilter-class | Create a NullFilter object |
| PearsonSolver | Create a Solver class object using Pearson correlation... |
| PearsonSolver-class | An S4 class to represent a Pearson solver |
| RandomForestSolver | Create a Solver class object using the Random Forest solver |
| RandomForestSolver-class | Class RandomForestSolver |
| rescalePredictorWeights | Rescale the Predictor Weights |
| RidgeSolver | Create a Solver class object using the Ridge solver |
| RidgeSolver-class | Class RidgeSolver |
| solve | Solve a TReNA Object |
| solve.BayesSpike | Run the Bayes Spike Solver |
| solve.Ensemble | Run the Ensemble Solver |
| solve.Lasso | Run the LASSO Solver |
| solve.LassoPV | Run the LASSO P-Value Solver |
| solve.Pearson | Run the Pearson Solver |
| solve.RandomForest | Run the Random Forest Solver |
| Solver-class | Define an object of class Solver |
| solve.Ridge | Run the Ridge Regression Solver |
| solve.Spearman | Run the Spearman Solver |
| solve.SqrtLasso | Run the Square Root LASSO Solver |
| SpearmanSolver | Create a Solver class object using Spearman correlation... |
| SpearmanSolver-class | An S4 class to represent a Spearman solver |
| SqrtLassoSolver | Create a Solver class object using the Square Root LASSO... |
| SqrtLassoSolver-class | An S4 class to represent a Square Root LASSO solver |
| TReNA-class | Class TReNA |
| TReNA-package | Inferring Transcriptional Regulation with TReNA |
| VarianceFilter-class | Create a VarianceFilter object |
