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

Documentation for package ‘TReNA’ version 0.99.10

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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