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


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Documentation for package ‘trena’ version 1.8.0

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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 Square Root LASSO 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.SqrtLassoSolver Run the Square Root LASSO 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 Square Root Lasso 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.SqrtLassoSolver Show the Square Root Lasso 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.SqrtLasso Run the Square Root LASSO 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
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 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
.SqrtLassoSolver An S4 class to represent a Square Root LASSO solver
.Trena Define an object of class Trena
.VarianceFilter Create a VarianceFilter object
.XGBoostSolver An S4 class to represent a XGBoost solver