% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mnsea_subnetwork.R
\name{extract_mnsea_subnetwork}
\alias{extract_mnsea_subnetwork}
\title{Extract pathway subnetwork data from a \code{mnseaResult}}
\usage{
extract_mnsea_subnetwork(
  res,
  pathway_id = NULL,
  include_couplings = TRUE,
  include_isolated = TRUE
)
}
\arguments{
\item{res}{A \code{mnseaResult} object.}

\item{pathway_id}{Optional pathway ID. If \code{NULL}, the top pathway is used.}

\item{include_couplings}{Logical, whether to include inter-layer coupling
edges. Default is \code{TRUE}.}

\item{include_isolated}{Logical, whether to keep nodes without retained
edges. Default is \code{TRUE}.}
}
\value{
A list with \code{pathway}, \code{layer_contribution}, \code{nodes}, and \code{edges}.
}
\description{
Extract pathway subnetwork data from a \code{mnseaResult}
}
