Difference between revisions of "Metabomatching"
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| + | == Metabomatching is a procedure to identify compounds from spectral features that jointly associate with genotypes.== | ||
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| + | '''Publication''' | ||
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| + | Metabomatching: Using genetic association to identify metabolites in proton NMR spectroscopy | ||
| + | [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005839 PLoS Comput Biol 13(12): e1005839] | ||
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'''Software''' | '''Software''' | ||
| − | * The simplest method to run metabomatching is to use the metabomatching docker image. With a working docker installation ([http://www.docker.com/products/overview get docker]), run <br/><code>docker pull | + | * The simplest method to run metabomatching is to use its implementation in the [http://phenomenal-h2020.eu/home/ PhenoMeNal] portal [http://public.phenomenal-h2020.eu/ 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. |
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| + | * Alternatively, the metabomatching docker image can be pulled and run locally. With a working docker installation ([http://www.docker.com/products/overview get docker]), run <br/><code>docker pull docker-registry.phenomenal-h2020.eu/phnmnl/metabomatching</code><br/>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, run<br/><code>docker run -i -v <absolute/path/to/my/directory>:/mm-ps metabomatching/metabomatching</code><br/>which will run metabomatching, and write results to <code><absolute/path/to/my/directory></code>. Note that on Windows, the absolute path must be formatted without using a colon, so to use the directory <code>C:\MyDir</code>, the path must be formatted as <code>//c/MyDir</code>, | ||
* To run metabomatching on your own pseudospectra, please refer to the documentation ([https://github.com/rrueedi/metabomatching-pre/blob/master/documentation/howto.pdf PDF]). | * To run metabomatching on your own pseudospectra, please refer to the documentation ([https://github.com/rrueedi/metabomatching-pre/blob/master/documentation/howto.pdf PDF]). | ||
| − | * To run metabomatching directly, on a system running either Matlab or octave, metabomatching can also be obtained from GitHub<br/><code>https://github.com/rrueedi/metabomatching | + | * 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<br/><code>https://github.com/rrueedi/metabomatching.git</code><br/> |
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The procedure was in applied in | The procedure was in applied in | ||
| − | * the metabolome-wide genome-wide association study in the CoLaus cohort [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004132 | + | * the metabolome-wide genome-wide association study in the CoLaus cohort [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004132 PLoS Genet, 10(2): e1004132] |
| − | * the metabolome-wide genome-wide association study in the SHIP cohort [http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005487 | + | * the metabolome-wide genome-wide association study in the SHIP cohort [http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005487 PLoS Genet 11(9): e1005487] |
Latest revision as of 13:47, 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
