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Compound ID lookup via pubchem

Source: R/hmdb_lookup_class.R
hmdb_lookup.Rd

Requests HMBD records based on HMDB identifiers.

Usage

hmdb_lookup(query_column, suffix = "_hmdb", output = "inchikey", ...)

Arguments

query_column

(character) The name of a column in the annotation table containing values to search in the api call.

suffix

(character) A suffix appended to all column names in the returned result. The default is "_hmdb".

output

(character) The value returned from the HMDB xml. The default is "inchikey".

...

Additional slots and values passed to struct_class.

Value

A hmdb_lookup object with the following output slots:

updated(annotation_source) The annotation_source after adding data returned by the API.

Details

This object makes use of functionality from the following packages:

  • XML

Inheritance

A hmdb_lookup object inherits the following struct classes:

[hmdb_lookup] -> [rest_api] -> [model] -> [struct_class]

References

Temple Lang D (2024). XML: Tools for Parsing and Generating XML Within R and S-Plus. R package version 3.99-0.16.1, https://CRAN.R-project.org/package=XML.

Examples

M <- hmdb_lookup(
        output = "inchikey",
        base_url = "http://www.hmdb.ca/metabolites",
        url_template = "<base_url>/<query_column>.xml",
        query_column = character(0),
        cache = NULL,
        status_codes = list(),
        delay = 0.5,
        suffix = "_rest_api")