Solver-class.RdThe Solver class is a base class that governs the different solvers available in trena.
It is rarely called by itself; rather, interaction with a particular solver object
is achieved using a specific solver type.
Solver(mtx.assay = matrix(), targetGene, candidateRegulators, quiet = TRUE)
| 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 |
| quiet | A logical indicating whether or not the Solver object should print output |
An object of the Solver class
getAssayData, getTarget, getRegulators
Other Solver class objects:
BayesSpikeSolver,
EnsembleSolver,
HumanDHSFilter-class,
LassoPVSolver,
LassoSolver,
PearsonSolver,
RandomForestSolver,
RidgeSolver,
SpearmanSolver,
SqrtLassoSolver,
XGBoostSolver
#' # Create a Solver object using the included Alzheimer's data load(system.file(package="trena", "extdata/ampAD.154genes.mef2cTFs.278samples.RData")) targetGene <- "MEF2C" candidateRegulators <- setdiff(rownames(mtx.sub), targetGene) solver <- Solver(mtx.sub, targetGene, candidateRegulators) # Create a simple Solver object with default options