solve.LassoPV: Run the LASSO P-Value Solver
In trena: Fit transcriptional regulatory networks using gene expression, priors, machine learning
Description
Usage
Arguments
Value
See Also
Examples
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
1
2
## 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
Other solver methods:
run,BayesSpikeSolver-method,
run,EnsembleSolver-method,
run,LassoSolver-method,
run,PearsonSolver-method,
run,RandomForestSolver-method,
run,RidgeSolver-method,
run,SpearmanSolver-method,
run,XGBoostSolver-method
Examples
1
2
3
4
5
6
# 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)
trena documentation built on Nov. 15, 2020, 2:07 a.m.
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Description Usage Arguments Value See Also Examples
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
1 2 | ## 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
Other solver methods:
run,BayesSpikeSolver-method,
run,EnsembleSolver-method,
run,LassoSolver-method,
run,PearsonSolver-method,
run,RandomForestSolver-method,
run,RidgeSolver-method,
run,SpearmanSolver-method,
run,XGBoostSolver-method
Examples
1 2 3 4 5 6 | # 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)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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