Difference between revisions of "Metabomatching"

Revision as of 17:27, 4 December 2017

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, run
docker 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 directory C:\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

@@ Line 1: / Line 1: @@
 '''''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
+[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005839 PLoS Comput Biol 13(12): e1005839]
 '''Software'''
@@ Line 15: / Line 21: @@
 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 PLOS Genet, 10(2): e1004132]
+* 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 PLOS Genet 11(9): e1005487]
+* 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]