prepare_gene_sets: Prepare gene sets for GSEA

In ggpicrust2: Make 'PICRUSt2' Output Analysis and Visualization Easier

Prepare gene sets for GSEA

Description

Prepare gene sets for GSEA

Usage

prepare_gene_sets(pathway_type = "KEGG", organism = "ko", go_category = "all")

Arguments

pathway_type	A character string specifying the pathway type: "KEGG", "MetaCyc", or "GO"
organism	Deprecated and has no effect; gene sets are KO-based for both KEGG and GO. See pathway_gsea for details. Retained for signature compatibility only.
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 table(ko_to_go_reference$category).

Value

A list of pathway gene sets

ggpicrust2 documentation built on April 30, 2026, 1:06 a.m.