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 generic class that governs the different solvers available in TReNA. A Solver class object is constructed during creation of a TReNA object and resides within the TReNA object. It is rarely called by itself; rather, interaction with a particular solver object is achieved using the solve method on a TReNA object.

Usage

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

## S4 method for signature 'Solver'
getAssayData(obj)

Arguments

mtx.assay	An assay matrix of gene expression data
quiet	A logical indicating whether or not the Solver object should print output
obj	An object of class Solver

Value

An object of the Solver class

Methods (by generic)

• getAssayData: Retrieve the assay matrix of gene expression data

See Also

getAssayData, TReNA, solve

Other Solver class objects: BayesSpikeSolver, EnsembleSolver, LassoPVSolver, LassoSolver, PearsonSolver, RandomForestSolver, RidgeSolver, SpearmanSolver, SqrtLassoSolver

Examples

# Create a simple Solver object with default options
mtx <- matrix(rnorm(10000), nrow = 100)
solver <- Solver(mtx)


# Create a Solver object using the included Alzheimer's data and retrieve the matrix
load(system.file(package="TReNA", "extdata/ampAD.154genes.mef2cTFs.278samples.RData"))
solver <- Solver(mtx.sub)
mtx <- getAssayData(solver)

TReNA documentation built on Nov. 17, 2017, 12:35 p.m.