enrich_kegg: enrich_kegg

In tidymass/metpath: Pathway analysis for metabolomics data

enrich_kegg

Description

Pathway enrichment for SMPDB database.

Usage

enrich_kegg(
  query_id,
  query_type = c("compound", "gene"),
  id_type = c("KEGG"),
  pathway_database,
  p_cutoff = 0.05,
  p_adjust_method = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr",
    "none"),
  method = c("hypergeometric", "fisher"),
  threads = 3
)

Arguments

query_id	The vector of query IDs.
query_type	"compound" or "gene"
id_type	HMDB
pathway_database	KEGG or other metabolomics pathway database.
p_cutoff	p_cutoff
p_adjust_method	p_adjust_method
method	Hypergeometric or fisher test.
threads	threads

Value

The MSE analysis result.

Author(s)

Xiaotao Shen [e-mail]

Examples

## Not run: 
data("kegg_hsa_pathway")

remain_idx <-
  kegg_hsa_pathway@pathway_class %>%
  unlist() %>%
  stringr::str_detect("Disease") %>%
  `!`() %>%
  which()

pathway_database <-
  filter_pathway(object = kegg_hsa_pathway,
                 remain_idx = remain_idx[1:50])

data("query_id_kegg")

object <-
  enrich_kegg(
    query_id = query_id_kegg,
    query_type = "compound",
    id_type = "KEGG",
    pathway_database = pathway_database,
    p_cutoff = 0.05,
    p_adjust_method = "BH",
    method = "hypergeometric",
    threads = 5
  )

object

## End(Not run)

tidymass/metpath documentation built on Sept. 24, 2022, 9:25 p.m.