BayesSpikeSolver {trena} | R Documentation

## Create a Solver class object using the Bayes Spike Solver

### Description

Create a Solver class object using the Bayes Spike Solver

### Usage

    BayesSpikeSolver(
      mtx.assay = matrix(),
      targetGene,
      candidateRegulators,
      nOrderings = 10,
      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 with the target gene
`nOrderings` | An integer denoting the number of random starts to use for the Bayes Spike method (default = 10)
`quiet` | A logical denoting whether or not the solver should print output

### Value

A Solver class object with Bayes Spike as the solver

### See Also

`solve.BayesSpike`, `getAssayData`

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

### Examples

    load(system.file(package="trena", "extdata/ampAD.154genes.mef2cTFs.278samples.RData"))
    target.gene <- "MEF2C"
    tfs <- setdiff(rownames(mtx.sub), target.gene)
    bayes.solver <- BayesSpikeSolver(mtx.sub, target.gene, tfs)

[Package trena version 1.14.0 Index]