run,SpearmanSolver-method {trena} | R Documentation

## Run the Spearman Solver

### Description

Given a TReNA object with Spearman as the solver, use the `cor` function with `method = "spearman"` to esimate coefficients for each transcription factor as a predictor of the target gene's expression level.

### Usage

    ## S4 method for signature 'SpearmanSolver'
    run(obj)

### Arguments

`obj` | An object of class SpearmanSolver

### Value

The set of Spearman Correlation Coefficients between each transcription factor and the target gene.

### See Also

`cor`, `SpearmanSolver`

Other solver methods: `run,BayesSpikeSolver-method`, `run,EnsembleSolver-method`, `run,LassoPVSolver-method`, `run,LassoSolver-method`, `run,PearsonSolver-method`, `run,RandomForestSolver-method`, `run,RidgeSolver-method`, `run,XGBoostSolver-method`

### Examples

    # Load included Alzheimer's data, create a TReNA object with Bayes Spike as solver, and solve
    load(system.file(package="trena", "extdata/ampAD.154genes.mef2cTFs.278samples.RData"))
    target.gene <- "MEF2C"
    tfs <- setdiff(rownames(mtx.sub), target.gene)
    spearman.solver <- SpearmanSolver(mtx.sub, target.gene, tfs)
    tbl <- run(spearman.solver)

[Package trena version 1.10.2 Index]