Annotates data from liquid chromatography coupled to mass spectrometry (LC/MS) metabolomics experiments. Based on a network algorithm (O.Senan, A. Aguilar- Mogas, M. Navarro, O. Yanes, R.Guimerà and M. Sales-Pardo, Metabolomics Conference (2016), Dublin), 'CliqueMS' builds a weighted similarity network where nodes are features and edges are weighted according to the similarity of this features. Then it searches for the most plausible division of the similarity network into cliques (fully connected components). Finally it annotates metabolites within each clique, obtaining for each annotated metabolite the neutral mass and their features, corresponding to isotopes, ionization adducts and fragmentation adducts of that metabolite.
| Version: | 0.3.0 |
| Depends: | R (≥ 3.4.0) |
| Imports: | Rcpp (≥ 0.12.15), xcms (≥ 3.0.0), MSnbase, igraph, qlcMatrix, Matrix, methods |
| LinkingTo: | Rcpp, BH, RcppArmadillo |
| Suggests: | knitr, rmarkdown, testthat, CAMERA |
| Published: | 2019-01-30 |
| Author: | Oriol Senan Campos [aut, cre], Antoni Aguilar-Mogas [aut], Jordi Capellades [aut], Miriam Navarro [aut], Oscar Yanes [aut], Roger Guimerà [aut], Marta Sales-Pardo [aut] |
| Maintainer: | Oriol Senan Campos <oriol.senan at urv.cat> |
| BugReports: | https://github.com/osenan/cliqueMS/issues |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: | https://github.com/osenan/cliqueMS |
| NeedsCompilation: | yes |
| SystemRequirements: | C++11 |
| Citation: | cliqueMS citation info |
| Materials: | README NEWS |
| CRAN checks: | cliqueMS results |
| Reference manual: | cliqueMS.pdf |
| Vignettes: |
Annotating LC/MS data with cliqueMS |
| Package source: | cliqueMS_0.3.0.tar.gz |
| Windows binaries: | r-devel: cliqueMS_0.3.0.zip, r-release: cliqueMS_0.3.0.zip, r-oldrel: cliqueMS_0.3.0.zip |
| OS X binaries: | r-release: not available, r-oldrel: not available |
| Old sources: | cliqueMS archive |
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