R implementation for mzTab-M

Welcome to RmzTabM!

This is the mzTab-M R API and reference implementation.

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.

📌 see the package vignette for examples and an introduction of the provided functionality.

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

• legacy rmzTabM package
• mzTab-M Standard Specification
• jmzTab-M Reference Implementation and Validator
• jmzTab-M Webapplication and Validator

Installation

The R package can be installed from GitHub using the following commands:

#' Install required packages
install.packages("devtools")
install.packages("BiocManager")

#' Install the repository
BiocManager::install("RforMassSpectrometry/RmzTabM")

🛠️ Development status

ℹ️ core functions are expected to take and return single base R data types.

• core functionality to format metadata (MTD section)
• core functionality to format small molecule feature (SMF section)
• core functionality to format the (SML section)
• core functionality to format the (SME section)
• core functionality to extract metadata from an mzTab-M file and reconstruct a sample/experiment data.frame
• core functionality to extract the SMF data table from an mzTab-M file
• core functionality to extract the SME data table from an mzTab-M file
• core functionality to extract the SML data table from an mzTab-M file
• high-level functionality to simplify exporting experimental data in mzTab-M format
• support for mzTab-M JSON format
• mzTab-M file validation

👀 see also the package NEWS for updates.

🤝 Contribution

Please help us improving and completing the package! Any type of contribution welcome 👐 - including discussions, suggestions or actual code. Don’t be afraid - we’re friendly ☺️! 👉 get involved by opening an issue.

Please also check out the RforMassSpectrometry Contributions Guide.

📜 Code of Conduct

We follow the RforMassSpectrometry Code of Conduct to maintain an inclusive and respectful community.

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🙌 Acknowledgements

We thank the many researchers contributing through discussions or through code. An potentially incomplete list of people:

TODO - add names of hackathon participants, etc.