metabolomicsWorkbenchR

A Bioconductor package for interfacing with the Metabolomics Workbench API (https://www.metabolomicsworkbench.org/).

Installation

To install this package, start R (version “4.0”) and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("metabolomicsWorkbenchR")

Alternatively, to install from github use the remotes package, where @master can be replaced with release tags if desired:

remotes::install_github('computational-metabolomics/metabolomicsWorkbenchR@master')

Introduction

This package enables access to the Metabolomics Workbench API (MWA) using a simple query interface. For example, the ‘study’ context can be queried using the ‘study_title’ input to search the database for all studies with the keyword ‘Diabetes’ in the title and return a summary:

library(metabolomicsWorkBench)
df = do_query(context = 'study', input_item = 'study_title', input_value = 'Diabetes', output_item = 'summary')

The query interface is designed to mirror the API documentation as closely as possible (https://www.metabolomicsworkbench.org/tools/MWRestAPIv1.0.pdf).

Methods have been included using multiple queries to coerce study data from the database into different data structures used within Bioconductor, namely SummarizedExperiment and MultiAssayExperiment.

In addition methods have been included to coerce study data into DatasetExperiment objects for compatibility with our struct and structToolbox packages (both available on Bioconductor).