solve.Spearman: Run the Spearman Solver

run,SpearmanSolver-methodR 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,BicorSolver-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)

PriceLab/trena documentation built on March 16, 2023, 10:01 a.m.