NetGreg (version 0.0.2)

NetworkGuided: NetworkGuided

Description

A main function to obtain network-guided penalized regression coefficient estimates.

Usage

NetworkGuided(Y, X, hubs, Z, nfolds = 5)

Value

A vector of network-guided penalized regression coefficients.

Arguments

Y

A continuous outcome variable.

X

A data matrix of dimension n x p representing samples (rows) by features (columns).

hubs

A vector of hubs idenfitied through identifyHubs function from our package.

Z

A matrix of clinical or demographic covariates.

nfolds

A user-specified numeric value for k-fold cross-validation.

Examples

library(plsgenomics)
data(Colon) ## Data from plsgenomics R package
X = data.frame(Colon$X[,1:100]) ## The first 100 genes
Z = data.frame(Colon$X[,101:102]) ## Two clinical covariates
colnames(Z) = c("Z1", "Z2")
Y = as.vector(Colon$X[,1000])  ## Continuous outcome variable

## Apply identifyHubs():
preNG = identifyHubs(X=X, delta=0.05, tau=5, ebic.gamma = 0.1)

## Explore preNG results:
hubs = preNG$hubs ## Returns the names of the identified hub nodes.

## Use our main NetworkGuided function, to obtain network-guided
## penalized regression coefficient estimates.
NG = NetworkGuided(Y=Y, X=X, hubs=preNG$hubs, Z=Z, nfolds=5)
NG$coef