enrich_kegg

Pathway enrichment for SMPDB database.

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

Xiaotao Shen shenxt1990@outlook.com

Examples

if (FALSE) {
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
}