Difference between revisions of "Metabomatching"
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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 | + | * 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 metabomatching/metabomatching-pre</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-pre</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 directly, on a system running either Matlab or octave, metabomatching can also be obtained from GitHub<br/><code>https://github.com/rrueedi/metabomatching-pre.git</code><br/> | |
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| − | <code>https://github.com/rrueedi/metabomatching-pre.git</code> | ||
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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] |
Revision as of 17:57, 1 February 2017
Metabomatching is a procedure to identify compounds from spectral features that jointly associate with genotypes.
Software
- The simplest method to run metabomatching is to use the metabomatching docker image. With a working docker installation (get docker), run
docker pull metabomatching/metabomatching-pre
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-pre
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, on a system running either Matlab or octave, metabomatching can also be obtained from GitHub
https://github.com/rrueedi/metabomatching-pre.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
