% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/get.gr.adj.R
\name{get.gr.adj}
\alias{get.gr.adj}
\title{Create an Adjacency Matrix of Gene Regulation with Propagation}
\usage{
get.gr.adj(t = 2)
}
\arguments{
\item{t}{An integer specifying the number of propagation steps. Default is 2.
If \code{t = 1}, the function returns the direct adjacency matrix without propagation.}
}
\value{
A numeric adjacency matrix representing the propagated gene regulatory
interactions. Each entry in the matrix reflects the weighted regulatory influence
of a transcription factor (TF) on a target gene, adjusted by consensus stimulation
and inhibition.
}
\description{
This function generates an adjacency matrix from a gene regulatory network
(\code{\link{gr.graph}}) with propagated regulatory effects. The propagation
iteratively multiplies the adjacency matrix to capture higher-order regulatory
interactions.
}
\details{
The function starts by modifying the weights of \code{\link{gr.graph}} edges to reflect
the regulatory effects. The edge weights are adjusted by multiplying the original
weights with the difference between the indicator attributes \code{consensus_stimulation} and
\code{consensus_inhibition}.

The resulting weighted adjacency matrix is then propagated by matrix
multiplication for \code{t} steps to capture indirect regulatory interactions.
Positive weights suggest stimulation effect, whereas negative weights indicate
inhibition effect
}
\examples{
# Generate an adjacency matrix with the default 2-step propagation
get.gr.adj()

# Generate an adjacency matrix with 3-step propagation
get.gr.adj(t = 3)

}
\seealso{
\code{\link{gr.graph}}
}
