solve.Lasso: Run the LASSO Solver
In trena: Fit transcriptional regulatory networks using gene expression, priors, machine learning
Description
Usage
Arguments
Value
See Also
Examples
Description
Given a LassoSolver object, use the glmnet 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 'LassoSolver'
run(obj)
Arguments
obj
An object of class LassoSolver
Value
A data frame containing the coefficients relating the target gene to each transcription factor, plus other fit parameters.
See Also
Other solver methods:
run,BayesSpikeSolver-method,
run,EnsembleSolver-method,
run,LassoPVSolver-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 LASSO 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)
lasso.solver <- LassoSolver(mtx.sub, target.gene, tfs)
tbl <- run(lasso.solver)
trena documentation built on Nov. 15, 2020, 2:07 a.m.
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.
Description Usage Arguments Value See Also Examples
Description
Given a LassoSolver object, use the glmnet 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 'LassoSolver'
run(obj)
|
Arguments
obj |
An object of class LassoSolver |
Value
A data frame containing the coefficients relating the target gene to each transcription factor, plus other fit parameters.
See Also
Other solver methods:
run,BayesSpikeSolver-method,
run,EnsembleSolver-method,
run,LassoPVSolver-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 LASSO 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)
lasso.solver <- LassoSolver(mtx.sub, target.gene, tfs)
tbl <- run(lasso.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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.