R/help.R

In TReNA: Fit transcriptional regulatory networks using gene expression, priors, machine learning

#' Inferring Transcriptional Regulation with TReNA
#'
#' 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
#'
#' TReNA Class Objects
#'
#' The \code{\link{TReNA}} class is the central piece of the package. It houses
#' the matrix of gene expression data as well as the details of the solver
#' chosen for feature selection. Its main method is \code{\link{solve}}, which
#' performs the feature selection and returns the resulting coefficients.
#'
#' Solver Class Objects 
#'
#'  The \code{\link{Solver}} class is a base class used within a
#' \code{\link{TReNA}} object. A particular \code{\link{Solver}} object
#' contains the name of the selected solver and dispatches the correct feature
#' selection method when \code{\link{solve}} is called on the \code{\link{TReNA}}
#' object. It is inherited by all the following subclasses, representing the
#' different feature selection methods: \code{\link{BayesSpikeSolver}},
#' \code{\link{EnsembleSolver}}, \code{\link{LassoPVSolver}},
#' \code{\link{LassoSolver}}, \code{\link{PearsonSolver}},
#' \code{\link{RandomForestSolver}}, \code{\link{RidgeSolver}},
#' \code{\link{SpearmanSolver}}, \code{\link{SqrtLassoSolver}}.
#' 
#' CandidateFilter Class Objects
#'
#' The \code{\link{CandidateFilter}} class is separate from the aforementioned
#' classes. It is a base class that contains a gene expression matrix and
#' is used to filter the transcription factors in the matrix. Filtering method
#' depends on the filter type chosen; there are currently the following
#' subclasses: \code{\link{FootprintFilter}}, \code{\link{NullFilter}},
#' \code{\link{VarianceFilter}}. The filters are applied using the
#' \code{\link{getCandidates}} method on a given \code{\link{CandidateFilter}}
#' object. 
#'
#' FootprintFinder Class Objects
#'
#' The  \code{\link{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 \code{\link{getCandidates}} method for a \code{\link{FootprintFilter}}
#' object. However, a  \code{\link{FootprintFinder}} object has many more
#' available methods that allow it to extract information more flexibly.
#' 
#' @name TReNA-package
#' @aliases TReNA-package
#'
#' @docType package
#'
#' @seealso \code{\link{TReNA}}
NULL