solve: Solve a TReNA Object

In TReNA: Fit transcriptional regulatory networks using gene expression, priors, machine learning

Description

A TReNA object contains an assay matrix with expression data for genes of interest and a string representing the chosen solver. The solve method runs the specified solver given a target gene and a designated set of transcription factors, returning a list of parameters that quantify the relationship between the transcription factors and the target gene.

Usage

## S4 method for signature 'TReNA'
solve(obj, target.gene, tfs, tf.weights = rep(1,
  length(tfs)), extraArgs = list())

Arguments

obj	An object of class TReNA
target.gene	A designated target gene that should be part of the mtx.assay data
tfs	The designated set of transcription factors that could be associated with the target gene.
tf.weights	A set of weights on the transcription factors (default = rep(1, length(tfs)))
extraArgs	Modifiers to the solver

Value

A data frame containing coefficients relating the target gene to each transcription factor

See Also

TReNA

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,SpearmanSolver-method, run,SqrtLassoSolver-method

Examples

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

TReNA documentation built on Nov. 17, 2017, 12:35 p.m.