Difference between revisions of "Metabomatching"
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We invented ''Metabomatching'' as a method to identify candidate compounds from genetic associations to NMR features. In our recently published paper in <a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005839"> Plos Computational Biology </a> we extensively tested our approach on a large collection of real GWAS association results and saw better discovery of confirmed pathways than with other popular methods. | We invented ''Metabomatching'' as a method to identify candidate compounds from genetic associations to NMR features. In our recently published paper in <a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005839"> Plos Computational Biology </a> we extensively tested our approach on a large collection of real GWAS association results and saw better discovery of confirmed pathways than with other popular methods. | ||
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Revision as of 13:42, 17 January 2018
Metabomatching is a procedure to identify compounds from spectral features that jointly associate with genotypes.
Publication
Metabomatching: Using genetic association to identify metabolites in proton NMR spectroscopy PLoS Comput Biol 13(12): e1005839
Software
- The simplest method to run metabomatching is to use its implementation in the PhenoMeNal portal public.phenomenal-h2020.eu, located in the NMR section. Because the PhenoMeNal implementation is designed for ease of use, some advanced features may not be accessible. A set of test data is provided.
- Alternatively, the metabomatching docker image can be pulled and run locally. With a working docker installation (get docker), run
docker pull docker-registry.phenomenal-h2020.eu/phnmnl/metabomatching
to download the metabomatching container. The download may take some time, as the container includes a full Linux OS, octave to run metabomatching, and inkscape to convert metabomatching figures from SVG to PDF. To run metabomatching on the included sample pseudospectrum, rundocker run -i -v <absolute/path/to/my/directory>:/mm-ps metabomatching/metabomatching
which will run metabomatching, and write results to<absolute/path/to/my/directory>. Note that on Windows, the absolute path must be formatted without using a colon, so to use the directoryC:\MyDir, the path must be formatted as//c/MyDir,
- To run metabomatching on your own pseudospectra, please refer to the documentation (PDF).
- To run metabomatching directly, fully featured, and fully up to date (on a system running either Matlab or octave), metabomatching can also be obtained from GitHub
https://github.com/rrueedi/metabomatching.git
Examples
The procedure was in applied in
- the metabolome-wide genome-wide association study in the CoLaus cohort PLoS Genet, 10(2): e1004132
- the metabolome-wide genome-wide association study in the SHIP cohort PLoS Genet 11(9): e1005487
Questions, Comments
contact metabomatching(at)unil(dot)ch
