KO_safe: Perform Significance Analysis of Function and Expression

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

Perform Significance Analysis of Function and Expression

Description

Perform Significance Analysis of Function and Expression

Usage

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.

Value

A data frame containing SAFE results for KO enrichment.

See Also

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

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"
  )
}

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