Solver-class {trena} | R Documentation

## Define an object of class Solver

### 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

[Package trena version 1.12.1 Index]