id_convert {fobitools} | 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")

[Package fobitools version 1.0.0 Index]