get_reporter_score: Calculate reporter score

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

Calculate reporter score

Description

Calculate reporter score

Usage

get_reporter_score(
  ko_stat,
  type = c("pathway", "module")[1],
  feature = "ko",
  threads = 1,
  modulelist = NULL,
  perm = 4999,
  verbose = TRUE,
  p.adjust.method2 = "BH",
  min_exist_KO = 3,
  max_exist_KO = 600
)

Arguments

ko_stat	ko_stat result from pvalue2zs
type	'pathway' or 'module' for default KOlist for microbiome, 'CC', 'MF', 'BP', 'ALL' for default GOlist for homo sapiens. And org in listed in 'https://www.genome.jp/kegg/catalog/org_list.html' such as 'hsa' (if your kodf is come from a specific organism, you should specify type here).
feature	one of 'ko', 'gene', 'compound'
threads	default 1
modulelist	NULL or customized modulelist dataframe, must contain 'id','K_num','KOs','Description' columns. Take the 'KOlist' as example, use custom_modulelist.
perm	permutation number, default: 4999.
verbose	logical
p.adjust.method2	p.adjust.method for the correction of ReporterScore, see p.adjust
min_exist_KO	min exist KO number in a pathway (default, 3, when a pathway contains KOs less than 3, there will be no RS)
max_exist_KO	max exist KO number in a pathway (default, 600, when a pathway contains KOs more than 600, there will be no RS)

Value

reporter_res data.frame

See Also

Other GRSA: combine_rs_res(), ko.test(), pvalue2zs(), reporter_score()

Examples

data("KO_abundance_test")
ko_pvalue <- ko.test(KO_abundance, "Group", metadata)
ko_stat <- pvalue2zs(ko_pvalue, mode = "directed")
reporter_s1 <- get_reporter_score(ko_stat, perm = 499)

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