cliqueMS: Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data

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.GuimerĂ  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 GuimerĂ  [aut], Marta Sales-Pardo [aut]
Maintainer: Oriol Senan Campos <oriol.senan at>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
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:, r-release:, r-oldrel:
OS X binaries: r-release: not available, r-oldrel: not available
Old sources: cliqueMS archive


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