Man pages for PriceLab/TReNA
Fit transcriptional regulatory networks using gene expression, priors, machine learning

addStatsadd PCA-based summary stats on all TFs in the model
addStatsSimpleadd PCA-based summary stats on all TFs in the model
assessSnpAssess the effect of a SNP using a Trena object
BayesSpikeSolverCreate a Solver class object using the Bayes Spike Solver
BayesSpikeSolver-classAn S4 class to represent a Bayes Spike solver
closeDatabaseConnectionsClose a Footprint Database Connection
createGeneModelFromRegulatoryRegionsCreate a model for a target gene using a Trena object
createGeneModelFromTfListCreate a model for a target gene using a Trena object
elasticNetSolverRun the Elastic Net Solvers
EnsembleSolverCreate a Solver class object using an ensemble of solvers
EnsembleSolver-classClass EnsembleSolver
findMatchesByChromosomalRegionFind Motif Matches by Chromosomal Region
FootprintFilter-classCreate a FootprintFilter object
FootprintFinder-classClass FootprintFinder
GeneOntologyFilter-classCreate a GeneOntologyFilter object
getAssayDataRetrieve the assay matrix of gene expression data from a...
getAvailableSolversGet the available solvers for use in trena
getCandidatesGet candidate genes using a CandidateFilter object
getCandidates-FootprintFilter-methodGet candidate genes using the footprint filter
getCandidates-GeneOntologyFilter-methodGet candidate genes using a gene ontology filter
getCandidates-HumanDHSFilter-methodGet candidate genes using a human DHS filter
getCandidates-VarianceFilter-methodGet candidate genes using the variance filter
getChromLocGet Chromosome Location
getCoveragewhat percentage of the variance is captured in the first two...
getEncodeRegulatoryTableNames-HumanDHSFilterGet Encode regulatory tables using a human DHS filter
getFootprintsForGeneGet Footprints for Gene
getFootprintsInRegionGet Footprints in a Region
getGeneModelTableColumnNamesRetrieve the column names in the gene model table for a Trena...
getGenePromoterRegionGet Gene Promoter Region
getGtfGeneBioTypesGet the List of Biotypes
getGtfMoleculeTypesGet the List of Molecule Types
getPfmsRetrieve the motifs from the pfms slot
getPromoterRegionsAllGenesGet Promoter Regions for All Genes
getProximalPromoterGrab the region of the proximal promoter for a given gene...
getRegulatorsRetrieve the candiate regulators from a Solver object
getRegulatoryChromosomalRegionsGet the regulatory chromosomal regions for a Trena object
getRegulatoryRegionsGet a table of regulatory regions for a Human DHS filter
getRegulatoryTableColumnNamesRetrieve the column names in the regulatory table for a Trena...
getSequenceRetrieve the Sequence for a Set of Regions
getSolverNamesRetrieve the solver names from an EnsembleSolver object
getTargetRetrieve the target gene from a Solver object
HumanDHSFilter-classCreate a HumanDHSFilter object
LassoPVSolverCreate a Solver class object using the LASSO P-Value solver
LassoPVSolver-classAn S4 class to represent a LASSO P-Value solver
LassoSolverCreate a Solver class object using the LASSO solver
LassoSolver-classClass LassoSolver
MotifMatcher-classCreate a MotifMatcher object
normalizeModeltransform a specific column to fit normal distribution
parseChromLocStringParse a string containing a chromosome and location on the...
parseDatabaseUriParse a string containing the information for connecting to a...
PCAMaxClass PCAMax
PearsonSolverCreate a Solver class object using Pearson correlation...
PearsonSolver-classAn S4 class to represent a Pearson solver
RandomForestSolverCreate a Solver class object using the Random Forest solver
RandomForestSolver-classClass RandomForestSolver
rescalePredictorWeightsRescale the Predictor Weights
RidgeSolverCreate a Solver class object using the Ridge solver
RidgeSolver-classClass RidgeSolver
runRun a Solver object to select features
show.BayesSpikeSolverShow the Bayes Spike Solver
show.EnsembleSolverShow the Ensemble Solver
show-HumanDHSFilter-methodShow the details of a human DHS filter
show.LassoPVSolverShow the Lasso PV Solver
show.LassoSolverShow the Lasso Solver
show.MotifMatcherShow a MotifMatcher object
show.PearsonSolverShow the Pearson Solver
show.RandomForestSolverShow the Random Forest Solver
show.RidgeSolverShow the Ridge Solver
show.SpearmanSolverShow the Spearman Solver
show.SqrtLassoSolverShow the Square Root Lasso Solver
show.XGBoostSolverShow the XGBoost Solver
solve.BayesSpikeRun the Bayes Spike Solver
solve.EnsembleRun the Ensemble Solver
solve.LassoRun the LASSO Solver
solve.LassoPVRun the LASSO P-Value Solver
solve.PearsonRun the Pearson Solver
solve.RandomForestRun the Random Forest Solver
Solver-classDefine an object of class Solver
solve.RidgeRun the Ridge Regression Solver
solve.SpearmanRun the Spearman Solver
solve.SqrtLassoRun the Square Root LASSO Solver
solve.XGBoostRun the XGBoost Solver
SpearmanSolverCreate a Solver class object using Spearman correlation...
SpearmanSolver-classAn S4 class to represent a Spearman solver
SqrtLassoSolverCreate a Solver class object using the Square Root LASSO...
SqrtLassoSolver-classAn S4 class to represent a Square Root LASSO solver
Trena-classDefine an object of class Trena
trena-packageInferring Transcriptional Regulation with TReNA
VarianceFilter-classCreate a VarianceFilter object
XGBoostSolverCreate a Solver class using gradient boosting (a regression...
XGBoostSolver-classAn S4 class to represent a XGBoost solver
PriceLab/TReNA documentation built on Nov. 20, 2019, 10:49 p.m.