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


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Documentation for package ‘TReNA’ version 0.99.10

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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