% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/pathway_gsea.R
\name{prepare_gene_sets}
\alias{prepare_gene_sets}
\title{Prepare gene sets for GSEA}
\usage{
prepare_gene_sets(pathway_type = "KEGG", organism = "ko", go_category = "all")
}
\arguments{
\item{pathway_type}{A character string specifying the pathway type: "KEGG", "MetaCyc", or "GO"}

\item{organism}{Deprecated and has no effect; gene sets are KO-based
for both KEGG and GO. See \code{\link{pathway_gsea}} for details.
Retained for signature compatibility only.}

\item{go_category}{A character string specifying the GO category to use.
"all" (default) uses all categories. Valid values are determined by
the reference data; see \code{table(ko_to_go_reference$category)}.}
}
\value{
A list of pathway gene sets
}
\description{
Prepare gene sets for GSEA
}
