Difference between revisions of "Metabomatching"
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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 | 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 | ||
| − | <code>docker run -i -v <absolute path to | + | <code>docker run -i -v <absolute/path/to/my/directory>:/mm-ps metabomatching/metabomatching-pre</code> |
| − | which will run metabomatching, and write results to <code><absolute path to | + | which will run metabomatching, and write results to <code><absolute/path/to/my/directory></code>. To run metabomatching on your own pseudospectra, please refer to the documentation. For a system running either Matlab or octave, metabomatching can also be obtained from GitHub |
<code>https://github.com/rrueedi/metabomatching-pre.git</code> | <code>https://github.com/rrueedi/metabomatching-pre.git</code> | ||
Revision as of 14:02, 28 October 2016
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, run
docker 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>. To run metabomatching on your own pseudospectra, please refer to the documentation. For 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-genome wide association study in the CoLaus cohort PLoS Genetics 2014, 10(2): e1004132
- the metabolome-genome wide association study in the SHIP cohort PLoS Genet 11(9): e1005487
Questions, Comments
contact metabomatching(at)unil(dot)ch
