A B C E F G H L M N P R S T V X misc
trena-package | Inferring Transcriptional Regulation with TReNA |
addStats | add PCA-based summary stats on all TFs in the model |
addStats-method | add PCA-based summary stats on all TFs in the model |
addStatsSimple | add PCA-based summary stats on all TFs in the model |
addStatsSimple-method | add PCA-based summary stats on all TFs in the model |
assessSnp | Assess the effect of a SNP using a Trena object |
assessSnp-method | Assess the effect of a SNP using a Trena object |
BicorSolver | Create a Solver class object using Bicor correlation coefficients as the solver |
BicorSolver-class | An S4 class to represent a Bicor solver |
CandidateFilter | CandidateFilter |
CandidateFilter-class | CandidateFilter |
closeDatabaseConnections | Close a Footprint Database Connection |
closeDatabaseConnections-method | Close a Footprint Database Connection |
createGeneModelFromRegulatoryRegions | Create a model for a target gene using a Trena object |
createGeneModelFromRegulatoryRegions-method | Create a model for a target gene using a Trena object |
createGeneModelFromTfList | Create a model for a target gene using a Trena object |
createGeneModelFromTfList-method | 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 |
findMatchesByChromosomalRegion | Find Motif Matches by Chromosomal Region |
findMatchesByChromosomalRegion-method | Find Motif Matches by Chromosomal Region |
FootprintFilter | Create a FootprintFilter object |
FootprintFilter-class | Create a FootprintFilter object |
FootprintFinder | Class FootprintFinder |
FootprintFinder-class | Class FootprintFinder |
GeneOntologyFilter | Create a GeneOntologyFilter object |
GeneOntologyFilter-class | Create a GeneOntologyFilter object |
getAssayData | Retrieve the assay matrix of gene expression data from a Solver object |
getAssayData-method | Retrieve the assay matrix of gene expression data from a Solver object |
getAvailableSolvers | Get the available solvers for use in trena |
getCandidates | Get candidate genes using a CandidateFilter object |
getCandidates-FootprintFilter | Get candidate genes using the footprint filter |
getCandidates-GeneOntologyFilter | Get candidate genes using a gene ontology filter |
getCandidates-HumanDHSFilter | Get candidate genes using a human DHS filter |
getCandidates-method | Get candidate genes using the footprint filter |
getCandidates-method | Get candidate genes using a gene ontology filter |
getCandidates-method | Get candidate genes using a human DHS filter |
getCandidates-method | Get candidate genes using the variance filter |
getCandidates-VarianceFilter | Get candidate genes using the variance filter |
getChromLoc | Get Chromosome Location |
getChromLoc-method | Get Chromosome Location |
getCoverage | what percentage of the variance is captured in the first two principal components? |
getCoverage-method | what percentage of the variance is captured in the first two principal components? |
getEncodeRegulatoryTableNames | Get Encode regulatory tables using a human DHS filter |
getEncodeRegulatoryTableNames-method | Get Encode regulatory tables using a human DHS filter |
getFootprintsForGene | Get Footprints for Gene |
getFootprintsForGene-method | Get Footprints for Gene |
getFootprintsInRegion | Get Footprints in a Region |
getFootprintsInRegion-method | Get Footprints in a Region |
getGeneModelTableColumnNames | Retrieve the column names in the gene model table for a Trena object |
getGeneModelTableColumnNames-method | Retrieve the column names in the gene model table for a Trena object |
getGenePromoterRegion | Get Gene Promoter Region |
getGenePromoterRegion-method | Get Gene Promoter Region |
getGtfGeneBioTypes | Get the List of Biotypes |
getGtfGeneBioTypes-method | Get the List of Biotypes |
getGtfMoleculeTypes | Get the List of Molecule Types |
getGtfMoleculeTypes-method | Get the List of Molecule Types |
getPfms | Retrieve the motifs from the pfms slot |
getPfms-method | Retrieve the motifs from the pfms slot |
getPromoterRegionsAllGenes | Get Promoter Regions for All Genes |
getPromoterRegionsAllGenes-method | Get Promoter Regions for All Genes |
getProximalPromoter | Grab the region of the proximal promoter for a given gene symbol |
getProximalPromoter-method | Grab the region of the proximal promoter for a given gene symbol |
getRegulators | Retrieve the candiate regulators from a Solver object |
getRegulators-method | Retrieve the candiate regulators from a Solver object |
getRegulatoryChromosomalRegions | Get the regulatory chromosomal regions for a Trena object |
getRegulatoryChromosomalRegions-method | Get the regulatory chromosomal regions for a Trena object |
getRegulatoryRegions | Get a table of regulatory regions for a Human DHS filter |
getRegulatoryRegions-method | Get a table of regulatory regions for a Human DHS filter |
getRegulatoryTableColumnNames | Retrieve the column names in the regulatory table for a Trena object |
getRegulatoryTableColumnNames-method | Retrieve the column names in the regulatory table for a Trena object |
getSequence | Retrieve the Sequence for a Set of Regions |
getSequence-method | Retrieve the Sequence for a Set of Regions |
getSolverNames | Retrieve the solver names from an EnsembleSolver object |
getSolverNames-method | Retrieve the solver names from an EnsembleSolver object |
getTarget | Retrieve the target gene from a Solver object |
getTarget-method | Retrieve the target gene from a Solver object |
HumanDHSFilter | Create a HumanDHSFilter 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 | Create a MotifMatcher object |
MotifMatcher-class | Create a MotifMatcher object |
normalizeModel | transform a specific column to fit normal distribution |
normalizeModel-method | transform a specific column to fit normal distribution |
parseChromLocString | Parse a string containing a chromosome and location on the genome |
parseDatabaseUri | Parse a string containing the information for connecting to a database |
PCAMax | Class PCAMax |
PearsonSolver | Create a Solver class object using Pearson correlation coefficients as the solver |
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 |
rescalePredictorWeights-method | 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 |
run-method | Run the Bicor Solver |
run-method | Run the Ensemble Solver |
run-method | Run the LASSO Solver |
run-method | Run the LASSO P-Value Solver |
run-method | Run the Pearson Solver |
run-method | Run the Random Forest Solver |
run-method | Run the Ridge Regression Solver |
run-method | Run the Spearman Solver |
run-method | Run the XGBoost Solver |
run.BicorSolver | Run the Bicor Solver |
run.EnsembleSolver | Run the Ensemble Solver |
run.LassoPVSolver | Run the LASSO P-Value Solver |
run.LassoSolver | Run the LASSO Solver |
run.PearsonSolver | Run the Pearson Solver |
run.RandomForestSolver | Run the Random Forest Solver |
run.RidgeSolver | Run the Ridge Regression Solver |
run.SpearmanSolver | Run the Spearman Solver |
run.XGBoostSolver | Run the XGBoost Solver |
show-HumanDHSFilter | Show the details of a human DHS filter |
show-method | Show the details of a human DHS filter |
show-method | Show the Bicor Solver |
show-method | Show the Ensemble Solver |
show-method | Show the Lasso PV Solver |
show-method | Show the Lasso Solver |
show-method | Show a MotifMatcher object |
show-method | Show the Pearson Solver |
show-method | Show the Random Forest Solver |
show-method | Show the Ridge Solver |
show-method | Show the Spearman Solver |
show-method | Show the XGBoost Solver |
show.BicorSolver | Show the Bicor Solver |
show.EnsembleSolver | Show the Ensemble Solver |
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 |
solve.Ridge | Run the Ridge Regression Solver |
solve.Spearman | Run the Spearman Solver |
solve.XGBoost | Run the XGBoost Solver |
Solver | Define an object of class Solver |
Solver-class | Define an object of class Solver |
SpearmanSolver | Create a Solver class object using Spearman correlation coefficients as the solver |
SpearmanSolver-class | An S4 class to represent a Spearman solver |
Trena | Define an object of class Trena |
Trena-class | Define an object of class Trena |
VarianceFilter | Create a VarianceFilter object |
VarianceFilter-class | Create a VarianceFilter object |
XGBoostSolver | Create a Solver class using gradient boosting (a regression technique) and the XGBoost library |
XGBoostSolver-class | An S4 class to represent a XGBoost solver |
.BicorSolver | An S4 class to represent a Bicor solver |
.CandidateFilter | CandidateFilter |
.EnsembleSolver | Class EnsembleSolver |
.FootprintFilter | Create a FootprintFilter object |
.FootprintFinder | Class FootprintFinder |
.GeneOntologyFilter | Create a GeneOntologyFilter object |
.HumanDHSFilter | Create a HumanDHSFilter object |
.LassoPVSolver | An S4 class to represent a LASSO P-Value solver |
.LassoSolver | Class LassoSolver |
.MotifMatcher | Create a MotifMatcher object |
.pcaMax | Class PCAMax |
.PearsonSolver | An S4 class to represent a Pearson solver |
.RandomForestSolver | Class RandomForestSolver |
.RidgeSolver | Class RidgeSolver |
.Solver | Define an object of class Solver |
.SpearmanSolver | An S4 class to represent a Spearman solver |
.Trena | Define an object of class Trena |
.VarianceFilter | Create a VarianceFilter object |
.XGBoostSolver | An S4 class to represent a XGBoost solver |