KO_padog: Perform Pathway Analysis with Down-weighting of Overlapping...

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

Perform Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)

Description

Perform Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)

Usage

KO_padog(
  reporter_res,
  verbose = TRUE,
  perm = 1000,
  p.adjust.method = "BH",
  ...
)

Arguments

reporter_res	The input reporter result.
verbose	If TRUE, print verbose messages. Default is TRUE.
perm	The number of permutations. Default is 1000.
p.adjust.method	Method for p-value adjustment. Default is "BH".
...	Additional parameters to be passed to padog function.

Value

A data frame containing PADOG results for KO enrichment.

A data frame with columns "ID," "Description," "K_num," "Exist_K_num," "p.value," and "p.adjust."

See Also

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

Examples

## use `PADOG` from the `PADOG` package.
if (requireNamespace("PADOG")) {
  data("reporter_score_res")
  padog_res <- KO_padog(reporter_score_res,
    verbose = TRUE,
    perm = 200, p.adjust.method = "none"
  )
}

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