Name Mode Size
.github 040000
R 040000
data-raw 040000
man 040000
tests 040000
vignettes 040000
.Rbuildignore 100644 0 kb
.gitignore 100644 1 kb
DESCRIPTION 100644 1 kb
NAMESPACE 100644 1 kb
NEWS 100644 0 kb 100644 2 kb
codecov.yml 100644 0 kb
<!-- badges: start --> [![Build Status](]( [![Codecov test coverage](]( <!-- badges: end --> # metabolomicsWorkbenchR A Bioconductor package for interfacing with the Metabolomics Workbench API ( ## Installation To install this package, start R (version "4.0") and enter: ```{r} 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: ```{r} 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: ```{r} 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 ( 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).