KO_fisher: Perform fisher's exact enrichment analysis

In ReporterScore: Generalized Reporter Score-Based Enrichment Analysis for Omics Data

Perform fisher's exact enrichment analysis

Description

Perform fisher's exact enrichment analysis

Usage

KO_fisher(
  ko_stat,
  padj_threshold = 0.05,
  logFC_threshold = NULL,
  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.
padj_threshold	p.adjust threshold to determine whether a feature significant or not. p.adjust < padj_threshold, default: 0.05
logFC_threshold	logFC threshold to determine whether a feature significant or not. abs(logFC)>logFC_threshold, default: NULL
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

Value

data.frame

See Also

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

Examples

## use `fisher.test` from the `stats` package.
data("reporter_score_res")
fisher_res <- KO_fisher(reporter_score_res)

ReporterScore documentation built on Sept. 11, 2024, 6:44 p.m.