All functions
|
|
BayesSpikeSolver-class
|
An S4 class to represent a Bayes Spike solver |
|
BayesSpikeSolver()
|
Create a Solver class object using the Bayes Spike Solver |
|
CandidateFilter()
|
CandidateFilter |
|
EnsembleSolver-class
|
Class EnsembleSolver |
|
EnsembleSolver()
|
Create a Solver class object using an ensemble of solvers |
|
FootprintFilter()
|
Create a FootprintFilter object |
|
FootprintFinder()
|
Class FootprintFinder |
|
GeneOntologyFilter()
|
Create a GeneOntologyFilter object |
|
HumanDHSFilter()
|
Create a HumanDHSFilter object |
|
LassoPVSolver-class
|
An S4 class to represent a LASSO P-Value solver |
|
LassoPVSolver()
|
Create a Solver class object using the LASSO P-Value solver |
|
LassoSolver-class
|
Class LassoSolver |
|
LassoSolver()
|
Create a Solver class object using the LASSO solver |
|
MotifMatcher()
|
Create a MotifMatcher object |
|
PCAMax()
|
Class PCAMax |
|
PearsonSolver-class
|
An S4 class to represent a Pearson solver |
|
PearsonSolver()
|
Create a Solver class object using Pearson correlation coefficients as the solver |
|
RandomForestSolver-class
|
Class RandomForestSolver |
|
RandomForestSolver()
|
Create a Solver class object using the Random Forest solver |
|
RidgeSolver-class
|
Class RidgeSolver |
|
RidgeSolver()
|
Create a Solver class object using the Ridge solver |
|
Solver()
|
Define an object of class Solver |
|
SpearmanSolver-class
|
An S4 class to represent a Spearman solver |
|
SpearmanSolver()
|
Create a Solver class object using Spearman correlation coefficients as the solver |
|
SqrtLassoSolver-class
|
An S4 class to represent a Square Root LASSO solver |
|
SqrtLassoSolver()
|
Create a Solver class object using the Square Root LASSO solver |
|
Trena()
|
Define an object of class Trena |
|
VarianceFilter()
|
Create a VarianceFilter object |
|
XGBoostSolver-class
|
An S4 class to represent a XGBoost solver |
|
XGBoostSolver()
|
Create a Solver class using gradient boosting (a regression technique) and the XGBoost library |
|
addStats(<PCAMax>)
|
add PCA-based summary stats on all TFs in the model |
|
addStatsSimple(<PCAMax>)
|
add PCA-based summary stats on all TFs in the model |
|
assessSnp(<Trena>)
|
Assess the effect of a SNP using a Trena object |
|
closeDatabaseConnections(<FootprintFinder>)
|
Close a Footprint Database Connection |
|
createGeneModelFromRegulatoryRegions(<Trena>)
|
Create a model for a target gene using a Trena object |
|
createGeneModelFromTfList(<Trena>)
|
Create a model for a target gene using a Trena object |
|
elasticNetSolver()
|
Run the Elastic Net Solvers |
|
findMatchesByChromosomalRegion(<MotifMatcher>)
|
Find Motif Matches by Chromosomal Region |
|
getAssayData(<Solver>)
|
Retrieve the assay matrix of gene expression data from a Solver object |
|
getAvailableSolvers()
|
Get the available solvers for use in trena |
|
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(<VarianceFilter>)
|
Get candidate genes using the variance filter |
|
getCandidates()
|
Get candidate genes using a CandidateFilter object |
|
getChromLoc(<FootprintFinder>)
|
Get Chromosome Location |
|
getCoverage(<PCAMax>)
|
what percentage of the variance is captured in the first two principal components? |
|
getEncodeRegulatoryTableNames(<HumanDHSFilter>)
|
Get Encode regulatory tables using a human DHS filter |
|
getFootprintsForGene(<FootprintFinder>)
|
Get Footprints for Gene |
|
getFootprintsInRegion(<FootprintFinder>)
|
Get Footprints in a Region |
|
getGeneModelTableColumnNames(<Trena>)
|
Retrieve the column names in the gene model table for a Trena object |
|
getGenePromoterRegion(<FootprintFinder>)
|
Get Gene Promoter Region |
|
getGtfGeneBioTypes(<FootprintFinder>)
|
Get the List of Biotypes |
|
getGtfMoleculeTypes(<FootprintFinder>)
|
Get the List of Molecule Types |
|
getPfms(<MotifMatcher>)
|
Retrieve the motifs from the pfms slot |
|
getPromoterRegionsAllGenes(<FootprintFinder>)
|
Get Promoter Regions for All Genes |
|
getProximalPromoter(<Trena>)
|
Grab the region of the proximal promoter for a given gene symbol |
|
getRegulators(<Solver>)
|
Retrieve the candiate regulators from a Solver object |
|
getRegulatoryChromosomalRegions(<Trena>)
|
Get the regulatory chromosomal regions for a Trena object |
|
getRegulatoryRegions(<HumanDHSFilter>)
|
Get a table of regulatory regions for a Human DHS filter |
|
getRegulatoryTableColumnNames(<Trena>)
|
Retrieve the column names in the regulatory table for a Trena object |
|
getSequence(<MotifMatcher>)
|
Retrieve the Sequence for a Set of Regions |
|
getSolverNames(<EnsembleSolver>)
|
Retrieve the solver names from an EnsembleSolver object |
|
getTarget(<Solver>)
|
Retrieve the target gene from a Solver object |
|
normalizeModel(<PCAMax>)
|
transform a specific column to fit normal distribution |
|
parseChromLocString()
|
Parse a string containing a chromosome and location on the genome |
|
parseDatabaseUri()
|
Parse a string containing the information for connecting to a database |
|
rescalePredictorWeights(<Solver>)
|
Rescale the Predictor Weights |
|
run()
|
Run a Solver object to select features |
|
show(<HumanDHSFilter>)
|
Show the details of a human DHS filter |
|
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 |
|
run(<BayesSpikeSolver>)
|
Run the Bayes Spike Solver |
|
run(<EnsembleSolver>)
|
Run the Ensemble Solver |
|
run(<LassoSolver>)
|
Run the LASSO Solver |
|
run(<LassoPVSolver>)
|
Run the LASSO P-Value 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 |
|
trena-package
|
Inferring Transcriptional Regulation with TReNA |