pathway_search: Query KEGG pathways for a given set of metabolites

In phoenics: Pathways Longitudinal and Differential Analysis in Metabolomics

Query KEGG pathways for a given set of metabolites

Description

Query KEGG pathways for a given set of metabolites

Usage

pathway_search(metab, organism, min_size = 2)

Arguments

metab	vector of metabolite KEGG codes
organism	organism code in KEGG database
min_size	minimal number of metabolites required for a pathway to be returned

Value

a data.frame with metabolites in rows and the following information in columns:

• metabolite_code metabolite code

• metabolite_name metabolite name

• pathway_code pathway code (identifier)

• pathway_name name of the pathway

Author(s)

Camille Guilmineau <[e-mail]>
Remi Servien <[e-mail]>
Nathalie Vialaneix <[e-mail]>

References

Kanehisa M., Goto S. (2000). KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Research, Volume 28, Issue 1, Pages 27–30, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/nar/28.1.27")}

Tenenbaum D., Maintainer B. (2022). KEGGREST: Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG). R package version 1.38.0.

Examples

if (requireNamespace("KEGGREST", quietly = TRUE)) {
  data("MTBLS422")
  quantif <- from_ASICS_to_PHOENICS(quantif)
  
  pathways <- pathway_search(metab = colnames(quantif), organism = "mmu")
  
}

phoenics documentation built on Sept. 11, 2024, 6:32 p.m.