id_convert: Convert Metabolite Identifiers
In pcastellanoescuder/FOBIEnrichR: Tools for Manipulating the FOBI Ontology

View source: R/id_convert.R

id_convert

R Documentation

Convert Metabolite Identifiers

Description

This function can convert metabolite identifiers to other available IDs in FOBI. Input vector can be a combination of different IDs.

Usage

id_convert(ids, to = "FOBI", fobi = fobitools::fobi)

Arguments

`ids`	A vector with metabolite IDs to convert. Input ID types can be FOBI, raw metabolite names (used in FOBI), HMDB, KEGG, PubChemCID, InChIKey, InChICode, ChemSpider, and a combination of them.
`to`	Target ID type. If possible, metabolites will be converted to this ID type. Options are "FOBI" (default), "metaboliteNames", "HMDB", "KEGG", "PubChemCID", "InChIKey", "InChICode", and "ChemSpider".
`fobi`	FOBI table obtained with 'parse_fobi()'. If this value is set to NULL, the last version of FOBI will be downloaded from GitHub.

Value

A tibble with input IDs and converted IDs.

Author(s)

Pol Castellano-Escuder

References

Pol Castellano-Escuder, Raúl González-Domínguez, David S Wishart, Cristina Andrés-Lacueva, Alex Sánchez-Pla, FOBI: an ontology to represent food intake data and associate it with metabolomic data, Database, Volume 2020, 2020, baaa033, https://doi.org/10.1093/databa/baaa033.

Examples


ids <- c(fobitools::idmap$HMDB[1:10], 
         fobitools::idmap$KEGG[11:23], 
         fobitools::idmap$InChIKey[100:150])
fobitools::id_convert(ids, to = "FOBI")

pcastellanoescuder/FOBIEnrichR documentation built on Oct. 21, 2024, 5:33 a.m.