KO_safe function

Perform Significance Analysis of Function and Expression

KO_safe(
  reporter_res,
  verbose = TRUE,
  perm = 1000,
  C.matrix = NULL,
  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.
• C.matrix: The contrast matrix. Default is NULL, and it will be generated from the module list.
• p.adjust.method: Method for p-value adjustment. Default is "BH".
• ...: Additional parameters to be passed to safe function.

Returns

A data frame containing SAFE results for KO enrichment.

Examples

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

See Also

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