solve.Spearman.RdGiven 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.
# S4 method for SpearmanSolver run(obj)
| obj | An object of class SpearmanSolver |
|---|
The set of Spearman Correlation Coefficients between each transcription factor and the target gene.
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,SqrtLassoSolver-method,
run,XGBoostSolver-method
# 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)