trena-package.Rd`trena` provides a framework for using gene expression data to infer relationships between a target gene and a set of transcription factors. It does so using a several classes and their associated methods, briefly documented below
#' Solver Class Objects
The Solver class is a base class used within `trena`. A particular
Solver object also contains the name of the selected solver and
dispatches the correct feature selection method when run is called on the
object. It is inherited by all the following subclasses, representing the
different feature selection methods: BayesSpikeSolver,
EnsembleSolver, LassoPVSolver,
LassoSolver, PearsonSolver,
RandomForestSolver, RidgeSolver,
SpearmanSolver, SqrtLassoSolver.
CandidateFilter Class Objects
The CandidateFilter class is a base class that is generally used to filter
the transcription factors in the expression matrix to obtain a set of candidate
regulators. Filtering method depends on the filter type chosen; there are currently the
following subclasses: FootprintFilter, HumanDHSFilter,
GeneOntologyFilter, and VarianceFilter. The filters are
applied using the getCandidates method on a given
CandidateFilter object.
FootprintFinder Class Objects
The FootprintFinder class is designed to allow extraction
of gene footprinting information from existing PostgreSQL or SQLite
databases. In standard use of the `trena` package, it is used solely by
the getCandidates method for a FootprintFilter
object. However, a FootprintFinder object has many more
available methods that allow it to extract information more flexibly.