KO_gsa: Perform gene set analysis

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

Perform gene set analysis

Description

Perform gene set analysis

Usage

KO_gsa(
  reporter_res,
  method = "Two class unpaired",
  p.adjust.method = "BH",
  verbose = TRUE,
  perm = 1000,
  ...
)

Arguments

reporter_res	reporter_res
method	Problem type: "quantitative" for a continuous parameter; "Two class unpaired" ; "Survival" for censored survival outcome; "Multiclass" : more than 2 groups, coded 1,2,3...; "Two class paired" for paired outcomes, coded -1,1 (first pair), -2,2 (second pair), etc
p.adjust.method	"BH"
verbose	TRUE
perm	1000
...	additional parameters to GSA

Value

enrich_res object

See Also

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

Examples

## use `GSA` from the `GSA` package.
if (requireNamespace("GSA")) {
  data("reporter_score_res")
  gsa_res <- KO_gsa(reporter_score_res, p.adjust.method = "none", perm = 200)
  plot(gsa_res)
}

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