KO_gsea function

Perform gene set enrichment analysis

KO_gsea(
  ko_stat,
  weight = "logFC",
  add_mini = NULL,
  p.adjust.method = "BH",
  type = c("pathway", "module")[1],
  feature = "ko",
  modulelist = NULL,
  verbose = TRUE
)

Arguments

• ko_stat: ko_stat dataframe from ko.test.
• weight: the metric used for ranking, default: logFC
• add_mini: add_mini when calculate the logFC. e.g (10+0.1)/(0+0.1), default 0.05*min(avg_abundance)
• p.adjust.method: The method used for p-value adjustment (default: "BH").
• type: "pathway" or "module" for default KOlist_file.
• feature: one of "ko", "gene", "compound"
• modulelist: NULL or customized modulelist dataframe, must contain "id","K_num","KOs","Description" columns. Take the KOlist as example, use custom_modulelist.
• verbose: logical

Returns

DOSE object

Examples

message("The following example require some time to run:")

## use `GSEA` from the `clusterProfiler` package.
if (requireNamespace("clusterProfiler")) {
  data("reporter_score_res")
  gsea_res <- KO_gsea(reporter_score_res, p.adjust.method = "none")
  enrichplot::gseaplot(gsea_res, geneSetID = data.frame(gsea_res)$ID[1])
  gsea_res_df <- as.enrich_res(gsea_res)
  plot(gsea_res_df)
}

See Also

Other common_enrich: KO_enrich(), KO_fisher(), KO_gsa(), KO_gsva(), KO_padog(), KO_safe(), KO_sea(), plot_enrich_res()