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

## Documentation for package ‘trena’ version 1.14.0

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

## Help Pages

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

trena-package | Inferring Transcriptional Regulation with TReNA

## -- A --

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

## -- 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
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

## -- E --

elasticNetSolver | Run the Elastic Net Solvers
EnsembleSolver | Create a Solver class object using an ensemble of solvers
EnsembleSolver-class | Class EnsembleSolver

## -- F --

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

## -- G --

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

## -- H --

HumanDHSFilter | Create a HumanDHSFilter object
HumanDHSFilter-class | Create a HumanDHSFilter object

## -- 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 --

MotifMatcher | Create a MotifMatcher object
MotifMatcher-class | Create a MotifMatcher object

## -- N --

normalizeModel | transform a specific column to fit normal distribution
normalizeModel-method | transform a specific column to fit normal distribution

## -- P --

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

## -- 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 | Run a Solver object to select features
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 XGBoost 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.XGBoostSolver | Run the XGBoost Solver

## -- S --

show-HumanDHSFilter | Show the details of a human DHS filter
show-method | Show the details of a human DHS filter
show-method | Show the Bayes Spike 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.BayesSpikeSolver | Show the Bayes Spike 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.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.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

## -- T --

Trena | Define an object of class Trena
Trena-class | Define an object of class Trena

## -- V --

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

## -- X --

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

## -- misc --

.BayesSpikeSolver | An S4 class to represent a Bayes Spike 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