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Convert to/from kegg identifiers

Source: R/mwb_compound_lookup_class.R
mwb_compound_lookup.Rd

Searches MetabolomicsWorkbench for compound identifiers.

Usage

mwb_compound_lookup(
  input_item = "inchi_key",
  query_column,
  output_item = "pubchem_id",
  suffix = "_mwb",
  ...
)

Arguments

input_item

(character) A valid input item for the compound context (see https://www.metabolomicsworkbench.org/tools/mw_rest.php). The values in the query_column should be of this type. The default is "inchi_key".

query_column

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

output_item

(character) A comma separated list of Valid output items for the compound context (see https://www.metabolomicsworkbench.org/tools/mw_rest.php). The default is "pubchem_id".

suffix

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

...

Additional slots and values passed to struct_class.

Value

A mwb_compound_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:

  • metabolomicsWorkbenchR

  • dplyr

Inheritance

A mwb_compound_lookup object inherits the following struct classes:

mwb_compound_lookup() ⭢ rest_api() ⭢ model() ⭢ struct_class()

References

Lloyd GR, Weber RJM (2023). metabolomicsWorkbenchR: Metabolomics Workbench in R. doi:10.18129/B9.bioc.metabolomicsWorkbenchR https://doi.org/10.18129/B9.bioc.metabolomicsWorkbenchR, R package version 1.12.0, https://bioconductor.org/packages/metabolomicsWorkbenchR.

Wickham H, François R, Henry L, Müller K, Vaughan D (2023). dplyr: A Grammar of Data Manipulation. R package version 1.1.3, https://CRAN.R-project.org/package=dplyr.

See also

Other REST API's: classyfire_lookup, kegg_lookup, lipidmaps_lookup, rest_api

Examples

M = mwb_compound_lookup(
      input_item = "inchi_key",
      output_item = "inchi_key",
      base_url = "https://www.metabolomicsworkbench.org/rest",
      url_template = "<base_url>/compound/<input_item>/<query_column>/<output_item>",
      query_column = character(0),
      cache = NULL,
      status_codes = list(),
      delay = 0.5,
      suffix = "_rest_api")