RidgeSolver: Create a Solver class object using the Ridge solver

Description Usage Arguments Value See Also Examples

Description

Create a Solver class object using the Ridge solver

Usage

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RidgeSolver(mtx.assay = matrix(), targetGene, candidateRegulators,
  regulatorWeights = rep(1, length(candidateRegulators)), alpha = 0,
  lambda = numeric(0), keep.metrics = FALSE, quiet = TRUE)

Arguments

mtx.assay

An assay matrix of gene expression data

targetGene

A designated target gene that should be part of the mtx.assay data

candidateRegulators

The designated set of transcription factors that could be associated with the target gene

regulatorWeights

A set of weights on the transcription factors (default = rep(1, length(tfs)))

alpha

A parameter from 0-1 that determines the proportion of LASSO to ridge used in the elastic net solver, with 0 being fully ridge and 1 being fully LASSO (default = 0.9)

lambda

A tuning parameter that determines the severity of the penalty function imposed on the elastic net regression. If unspecified, lambda will be determined via permutation testing (default = numeric(0)).

keep.metrics

A logical denoting whether or not to keep the initial supplied metrics versus determining new ones

quiet

A logical denoting whether or not the solver should print output

Value

A Solver class object with Ridge as the solver

See Also

solve.Ridge, getAssayData

Other Solver class objects: BayesSpikeSolver, EnsembleSolver, HumanDHSFilter-class, LassoPVSolver, LassoSolver, PearsonSolver, RandomForestSolver, Solver-class, SpearmanSolver, SqrtLassoSolver

Examples

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load(system.file(package="trena", "extdata/ampAD.154genes.mef2cTFs.278samples.RData"))
target.gene <- "MEF2C"
tfs <- setdiff(rownames(mtx.sub), target.gene)
ridge.solver <- RidgeSolver(mtx.sub, target.gene, tfs)

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