% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/getPathIDs.R
\name{getPathIDs}
\alias{getPathIDs}
\title{Retrieve and Classify Organism-Specific KEGG Pathways}
\usage{
getPathIDs(organism_code)
}
\arguments{
\item{organism_code}{Character vector of KEGG organism codes.}
}
\value{
A \code{data.frame} with columns:
\describe{
\item{Path_id}{Full KEGG pathway ID.}
\item{Path_description}{Full KEGG pathway name.}
\item{Path_category}{Top-level and subcategory from KEGG BRITE hierarchy.}
\item{Path_type}{\code{"metabolic"} or \code{"signaling"}, based on top-level category.}
\item{Species}{KEGG organism code.}
}
}
\description{
Retrieves KEGG pathway IDs for one or more organisms and assigns each to a
functional category and type based on KEGG BRITE hierarchy.
}
\details{
Pathway classification uses the KEGG BRITE hierarchy \code{br08901}.
Pathways under the top-level category \code{"Metabolism"} are typed as
\code{"metabolic"}; all others are typed as \code{"signaling"}. Global
and overview maps are excluded from the output.
}
\examples{
## 1) Retrieve all human pathways and filter for tryptophan metabolism
path_hsa <- getPathIDs("hsa")
trp_hsa <- subset(path_hsa, grepl("Tryptophan metabolism", Path_description))
head(trp_hsa)

## 2) Retrieve pathways for multiple organisms
org_vec <- c("hsa", "eco", "bsu")
path_multi <- getPathIDs(org_vec)

## 3) Show pathways shared across the selected organisms
##    (appear once per species, so shared ones have count == length(org_vec))
shared_counts <- table(path_multi$Path_description)
head(shared_counts[shared_counts == length(org_vec)])

## 4) Filter tryptophan metabolism pathways and show which species contain them
trp_multi <- subset(path_multi, grepl("Tryptophan metabolism", Path_description))
head(trp_multi)
table(trp_multi$Species)

}
\seealso{
\code{\link{buildKeggNetwork}} for building networks from these pathway sets.
}
