R implementation for mzTab-M

This is the mzTab-M reference implementation and validation API service.

NOTE: This is an early development version, please use at your own risk and report issues to help improve it!

mzTab-M is intended as a reporting standard for quantitative results from metabolomics/lipodomics approaches. This format is further intended to provide local LIMS systems as well as MS metabolomics repositories a simple way to share and combine basic information.

mzTab-M has been developed with a view to support the following general tasks:

1. Facilitate the sharing of final experimental results, especially with researchers outside the field of metabolomics.
2. Export of results to external software, including programs such as Microsoft Excel® and Open Office Spreadsheet and statistical software / coding languages such as R.
3. Act as an output format of (web-) services that report MS-based results and thus can produce standardized result pages.
4. Be able to link to the external experimental evidence e.g. by referencing back to mzML files.

Related Projects

• mzTab-M 2.0 Standard Specification
• jmzTab-M Reference Implementation and Validator
• jmzTab-M Webapplication and Validator

Overview

This API client was generated by the OpenAPI Generator project. By supplying the mzTab-M Specification, you can easily generate an API client, here for R:

docker run --rm \
    -v $PWD:/local openapitools/openapi-generator-cli generate \
    -i /local/mzTab_m_swagger.yml \
    -g r \
    -o /local/out/r

The output in out/r builds the basis of this package. Please note that for this implementation, the generated code was heavily modified.

Installation

You'll need the devtools package in order to build the API. Make sure you have a proper CRAN repository from which you can download packages.

Prerequisites

Install the devtools package with the following command.

if(!require(devtools)) { install.packages("devtools") }

Installation of the API package

Make sure you set the working directory to where the API code is located. Then execute

library(devtools)
install(".")

To run the tests, execute

library(devtools)
test()