Man pages for PriceLab/TReNA
Fit transcriptional regulatory networks using gene expression, priors, machine learning
| addStats | add PCA-based summary stats on all TFs in the model |
| addStatsSimple | add PCA-based summary stats on all TFs in the model |
| assessSnp | Assess the effect of a SNP using a Trena object |
| BicorSolver | Create a Solver class object using Bicor correlation... |
| BicorSolver-class | An S4 class to represent a Bicor solver |
| CandidateFilter-class | CandidateFilter |
| closeDatabaseConnections | Close a Footprint Database Connection |
| createGeneModelFromRegulatoryRegions | Create a model for a target gene using a Trena object |
| createGeneModelFromTfList | Create a model for a target gene using a Trena object |
| elasticNetSolver | Run the Elastic Net Solvers |
| EnsembleSolver | Create a Solver class object using an ensemble of solvers |
| EnsembleSolver-class | Class EnsembleSolver |
| FeatureTable | FeatureTable |
| findMatchesByChromosomalRegion | Find Motif Matches by Chromosomal Region |
| FootprintFilter-class | Create a FootprintFilter object |
| FootprintFinder-class | Class FootprintFinder |
| GeneOntologyFilter-class | Create a GeneOntologyFilter object |
| getAssayData | Retrieve the assay matrix of gene expression data from a... |
| getAvailableSolvers | Get the available solvers for use in trena |
| getCandidates | Get candidate genes using a CandidateFilter object |
| getCandidates-FootprintFilter-method | Get candidate genes using the footprint filter |
| getCandidates-GeneOntologyFilter-method | Get candidate genes using a gene ontology filter |
| getCandidates-HumanDHSFilter-method | Get candidate genes using a human DHS filter |
| getCandidates-VarianceFilter-method | Get candidate genes using the variance filter |
| getChromLoc | Get Chromosome Location |
| getCoverage | what percentage of the variance is captured in the first two... |
| getEncodeRegulatoryTableNames-HumanDHSFilter | Get Encode regulatory tables using a human DHS filter |
| getFootprintsForGene | Get Footprints for Gene |
| getFootprintsInRegion | Get Footprints in a Region |
| getGeneModelTableColumnNames | Retrieve the column names in the gene model table for a Trena... |
| getGenePromoterRegion | Get Gene Promoter Region |
| getGtfGeneBioTypes | Get the List of Biotypes |
| getGtfMoleculeTypes | Get the List of Molecule Types |
| getPfms | Retrieve the motifs from the pfms slot |
| getPromoterRegionsAllGenes | Get Promoter Regions for All Genes |
| getProximalPromoter | Grab the region of the proximal promoter for a given gene... |
| getRegulators | Retrieve the candiate regulators from a Solver object |
| getRegulatoryChromosomalRegions | Get the regulatory chromosomal regions for a Trena object |
| getRegulatoryRegions | Get a table of regulatory regions for a Human DHS filter |
| getRegulatoryTableColumnNames | Retrieve the column names in the regulatory table for a Trena... |
| getSequence | Retrieve the Sequence for a Set of Regions |
| getSolverNames | Retrieve the solver names from an EnsembleSolver object |
| getTarget | Retrieve the target gene from a Solver object |
| HumanDHSFilter-class | Create a HumanDHSFilter 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 |
| MotifMatcher-class | Create a MotifMatcher object |
| normalizeModel | transform a specific column to fit normal distribution |
| parseChromLocString | Parse a string containing a chromosome and location on the... |
| parseDatabaseUri | Parse a string containing the information for connecting to a... |
| PCAMax | Class PCAMax |
| 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 |
| run | Run a Solver object to select features |
| show.BicorSolver | Show the Bicor Solver |
| show.EnsembleSolver | Show the Ensemble Solver |
| show-HumanDHSFilter-method | Show the details of a human DHS filter |
| show.LassoPVSolver | Show the Lasso PV Solver |
| show.LassoSolver | Show the Lasso Solver |
| show.MotifMatcher | Show a MotifMatcher object |
| show.PearsonSolver | Show the Pearson Solver |
| show.RandomForestSolver | Show the Random Forest Solver |
| show.RidgeSolver | Show the Ridge Solver |
| show.SpearmanSolver | Show the Spearman Solver |
| show.XGBoostSolver | Show the XGBoost Solver |
| solve.Bicor | Run the Bicor 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.XGBoost | Run the XGBoost Solver |
| SpearmanSolver | Create a Solver class object using Spearman correlation... |
| SpearmanSolver-class | An S4 class to represent a Spearman solver |
| Trena-class | Define an object of class Trena |
| trena-package | Inferring Transcriptional Regulation with TReNA |
| VarianceFilter-class | Create a VarianceFilter object |
| XGBoostSolver | Create a Solver class using gradient boosting (a regression... |
| XGBoostSolver-class | An S4 class to represent a XGBoost solver |
