Run pathway enrichment analysis

Wrapper that runs ORA on consensus DE genes. Uses MSigDB Hallmark gene sets by default.

Usage

run_pathway_analysis(de_genes, method = "hallmark")

Arguments

de_genes

Consensus DE result from [find_consensus_genes()] with consensus_genes character vector and by_method list.

method

Gene set collection: "hallmark" (default), "kegg", "reactome", "go_bp".

Value

List with ORA results (see [run_ora()]).

See also

Other pathway: annotate_de_results(), annotate_genes(), plot_enrichment_barplot(), plot_enrichment_dotplot(), plot_gsea_running_score(), run_gsea(), run_ora()