Metabolomics Workbench study source

Imports the reported metabolite list for a Metabolomics Workbench study, using the metabolomicsWorkbenchR package. Only the identifiers a study depositor chose to report are returned as-is (e.g. metabolite_name, and where present refmet_name/pubchem_id/other_id) - no translation or enrichment is performed here. To reproduce the scenario of annotation software output that has names but no standardised identifiers (the case MetMashR's mashing steps are designed for), downstream workflow steps should use only the metabolite_name column and treat any pre-existing refmet_name/pubchem_id/other_id values as optional validation data, not as workflow input.

Usage

mwb_study_source(source, tag = "MWB", analysis_id = NULL, data = NULL, ...)

Arguments

source: (character) A Metabolomics Workbench study identifier e.g. "ST001039".
tag: (character) A (short) character string that is used to represent this source e.g. in column names or source columns when used in a workflow. The default is "MWB".
analysis_id: (character, NULL) Optionally restrict the imported metabolites to one or more specific analysis ids within the study (e.g. a single LC-MS assay). If NULL (the default), metabolites for all analyses in the study are returned. The default is NULL.
data: (data.frame, NULL) A data.frame of annotation data. The default is NULL.
...: Additional slots and values passed to struct_class.

Value

A mwb_study_source object. This object has no output slots.

Details

This object makes use of functionality from the following packages:

metabolomicsWorkbenchR

Inheritance

A mwb_study_source object inherits the following struct classes:

[mwb_study_source] -> [annotation_source] -> [struct_class]

References

Lloyd GR, Weber RJM (2026). metabolomicsWorkbenchR: Metabolomics Workbench in R. R package version 1.22.0.

Examples

M <- mwb_study_source(
        analysis_id = NULL,
        tag = character(0),
        data = data.frame(),
        source = character(0))