Solver-class: Define an object of class Solver

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

Description

The Solver class is a base class that governs the different solvers available in trena. It is rarely called by itself; rather, interaction with a particular solver object is achieved using a specific solver type.

Usage

Solver(mtx.assay = matrix(), targetGene, candidateRegulators, quiet = TRUE)

Arguments

mtx.assay	An assay matrix of gene expression data
targetGene	A designated target gene that should be part of the mtx.assay data
candidateRegulators	The designated set of transcription factors that could be associated
quiet	A logical indicating whether or not the Solver object should print output

Value

An object of the Solver class

See Also

getAssayData, getTarget, getRegulators

Other Solver class objects: BayesSpikeSolver, EnsembleSolver, HumanDHSFilter-class, LassoPVSolver, LassoSolver, PearsonSolver, RandomForestSolver, RidgeSolver, SpearmanSolver, XGBoostSolver

Examples

#' # Create a Solver object using the included Alzheimer's data
load(system.file(package="trena", "extdata/ampAD.154genes.mef2cTFs.278samples.RData"))
targetGene <- "MEF2C"
candidateRegulators <- setdiff(rownames(mtx.sub), targetGene)
solver <- Solver(mtx.sub, targetGene, candidateRegulators) # Create a simple Solver object with default options

trena documentation built on Nov. 15, 2020, 2:07 a.m.