solve.LassoPV: Run the LASSO P-Value Solver

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

Run the LASSO P-Value Solver

Description

Given a TReNA object with LASSO P-Value as the solver, use the lassopv function to estimate coefficients for each transcription factor as a predictor of the target gene's expression level.

Usage

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

Arguments

obj	An object of class LassoPVSolver

Value

A data frame containing the p-values for each transcription factor pertaining to the target gene plus the Pearson correlations between each transcription factor and the target gene.

See Also

lassopv, , LassoPVSolver

Other solver methods: run,BicorSolver-method, run,EnsembleSolver-method, run,LassoSolver-method, run,PearsonSolver-method, run,RandomForestSolver-method, run,RidgeSolver-method, run,SpearmanSolver-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)
lassopv.solver <- LassoPVSolver(mtx.sub, target.gene, tfs)
tbl <- run(lassopv.solver)

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