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Prepare gene sets for GSEA

Source: R/pathway_gsea.R
prepare_gene_sets.Rd

Prepare gene sets for GSEA

Usage

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

Arguments

pathway_type

A single 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 single 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