Description Usage Arguments Value See Also Examples
Create a Solver class object using Pearson correlation coefficients as the solver
1 2 | PearsonSolver(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 with the target gene |
quiet |
A logical denoting whether or not the solver should print output |
A Solver class object with Pearson correlation coefficients as the solver
Other Solver class objects: BayesSpikeSolver
,
EnsembleSolver
,
HumanDHSFilter-class
,
LassoPVSolver
, LassoSolver
,
RandomForestSolver
,
RidgeSolver
, Solver-class
,
SpearmanSolver
,
SqrtLassoSolver
1 2 3 4 | load(system.file(package="trena", "extdata/ampAD.154genes.mef2cTFs.278samples.RData"))
target.gene <- "MEF2C"
tfs <- setdiff(rownames(mtx.sub), target.gene)
pearson.solver <- PearsonSolver(mtx.sub, target.gene, tfs)
|
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