solve.Spearman: Run the Spearman Solver

In PriceLab/trena-until-01mar2018: Fit transcriptional regulatory networks using gene expression, priors, machine learning

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,SqrtLassoSolver-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-until-01mar2018 documentation built on May 25, 2019, 1:22 p.m.