Perform Significance Analysis of Function and Expression

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.

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

# \donttest{
## 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"
  )
}
#> Loading required namespace: safe
# }