% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/buildCrossSpeciesNetwork.R
\name{buildCrossSpeciesNetwork}
\alias{buildCrossSpeciesNetwork}
\title{Build Cross-Species MetaPathNet Network}
\usage{
buildCrossSpeciesNetwork(
  organism_codes,
  path_type = c("metabolic", "signaling", "integrated")
)
}
\arguments{
\item{organism_codes}{Character vector of KEGG organism codes
(e.g., "hsa" for \emph{Homo sapiens}, "eco" for \emph{E. coli}, "bsu" for \emph{Bacillus subtilis}).}

\item{path_type}{Character. One of:
\describe{
\item{"metabolic"}{Build network from metabolic pathways only.}
\item{"signaling"}{Build network from signaling pathways only.}
\item{"integrated"}{Combine both metabolic and signaling pathways into a single network.}
}}
}
\value{
A data frame representing the merged \emph{MetaPathNet network}, with three columns:
\describe{
\item{source}{Source node (KO, compound, or gene).}
\item{target}{Target node (KO, compound, or gene).}
\item{interaction_type}{Type of biological interaction or reaction.}
}
}
\description{
Constructs and merges \emph{MetaPathNet tables} (integrated metabolic and/or signaling networks)
across one or multiple KEGG organisms.
}
\details{
\itemize{
\item KEGG pathway lists are retrieved via \code{getPathIDs()} for all requested organisms.
\item Each species is processed separately, generating a species-specific MetaPathNet table
via \code{buildKeggNetwork()} according to \code{path_type}.
\item Species-level tables are then merged and deduplicated into a single cross-species network.
}
}
\examples{
## Cross-species metabolic network (human + E. coli strains)
## Note: Network construction can be time-consuming and depends on KEGG server response

host_microbe_code <- c("ece", "eco", "ecoo", "ecc", "ecs", "hsa")

\dontrun{
## Requires extensive KEGG API querying; runtime depends on server response
net_hsa_ecoli <- buildCrossSpeciesNetwork(
  organism_codes = host_microbe_code,
  path_type      = "metabolic"   # metabolic layer only
)
}

}
\seealso{
\code{\link{getPathIDs}} for retrieving pathway lists,
and \code{\link{buildKeggNetwork}} for building individual pathway networks.
}
