# Fit transcriptional regulatory networks using gene expression, priors, machine learning

## Documentation for package ‘TReNA’ version 0.99.10

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

B C E F G L M N P R S T V misc

TReNA-package | Inferring Transcriptional Regulation with TReNA

## -- B --

BayesSpikeSolver | Create a Solver class object using the Bayes Spike Solver
BayesSpikeSolver-class | An S4 class to represent a Bayes Spike solver

## -- C --

CandidateFilter | CandidateFilter
CandidateFilter-class | CandidateFilter
closeDatabaseConnections | Close a Footprint Database Connection
closeDatabaseConnections-method | Close a Footprint Database Connection

## -- E --

EnsembleSolver | Create a Solver class object using an ensemble of solvers
EnsembleSolver-class | Class EnsembleSolver

## -- F --

FootprintFilter | Create a FootprintFilter object
FootprintFilter-class | Create a FootprintFilter object
FootprintFinder | Class FootprintFinder
FootprintFinder-class | Class FootprintFinder

## -- G --

getAssayData | Retrieve the assay matrix of gene expression data from a Solver object
getAssayData-method | Define an object of class Solver
getCandidates | Get candidate genes using a CandidateFilter object
getCandidates-FootprintFilter | Get candidate genes using the variance filter
getCandidates-method | Get candidate genes using the variance filter
getCandidates-method | Get candidate genes using the null filter
getCandidates-method | Get candidate genes using the variance filter
getCandidates-NullFilter | Get candidate genes using the null filter
getCandidates-VarianceFilter | Get candidate genes using the variance filter
getChromLoc | Get Chromasome Location
getChromLoc-method | Get Chromasome Location
getFilterAssayData | Retrieve the assay matrix of gene expression data
getFilterAssayData-method | CandidateFilter
getFootprintsForGene | Get Footprints for Gene
getFootprintsForGene-method | Get Footprints for Gene
getFootprintsInRegion | Get Footprints in a Region
getFootprintsInRegion-method | Get Footprints in a Region
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
getPromoterRegionsAllGenes | Get Promoter Regions for All Genes
getPromoterRegionsAllGenes-method | Get Promoter Regions for All Genes
getSolverName | Get the Solver Name from a TReNA Object
getSolverName-method | Class TReNA
getSolverObject | Get the Solver Object from a TReNA Object
getSolverObject-method | Class TReNA

## -- L --

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

## -- M --

mapMotifsToTFsMergeIntoTable | Map Motifs to Transcription Factors and Merge into a Table
mapMotifsToTFsMergeIntoTable-method | Map Motifs to Transcription Factors and Merge into a Table

## -- N --

NullFilter | Create a NullFilter object
NullFilter-class | Create a NullFilter object

## -- P --

PearsonSolver | Create a Solver class object using Pearson correlation coefficients as the solver
PearsonSolver-class | An S4 class to represent a Pearson solver

## -- R --

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-method | Run the Bayes Spike 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 Square Root LASSO Solver
run.BayesSpikeSolver | Run the Bayes Spike 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.SqrtLassoSolver | Run the Square Root LASSO Solver

## -- S --

solve | Solve a TReNA Object
solve-method | 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
solve.Ridge | Run the Ridge Regression Solver
solve.Spearman | Run the Spearman Solver
solve.SqrtLasso | Run the Square Root LASSO Solver
solve.TReNA | Solve a TReNA Object
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
SqrtLassoSolver | Create a Solver class object using the Square Root LASSO solver
SqrtLassoSolver-class | An S4 class to represent a Square Root LASSO solver

## -- T --

TReNA | Class TReNA
TReNA-class | Class TReNA

## -- V --

VarianceFilter | Create a VarianceFilter object
VarianceFilter-class | Create a VarianceFilter object

## -- misc --

.BayesSpikeSolver | An S4 class to represent a Bayes Spike solver
.CandidateFilter | CandidateFilter
.EnsembleSolver | Class EnsembleSolver
.FootprintFilter | Create a FootprintFilter object
.FootprintFinder | Class FootprintFinder
.LassoPVSolver | An S4 class to represent a LASSO P-Value solver
.LassoSolver | Class LassoSolver
.NullFilter | Create a NullFilter object
.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
.SqrtLassoSolver | An S4 class to represent a Square Root LASSO solver
.TReNA | Class TReNA
.VarianceFilter | Create a VarianceFilter object