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.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.

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Package
cliqueMS
Type
Package
Title
Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data
Version
0.2.1
Date
2018-05-05
Description
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.
License
GPL (>= 2)
Depends
R (>= 3.4.0)
Imports
Rcpp (>= 0.12.15), xcms, igraph, qlcMatrix, Matrix, CAMERA, methods
LinkingTo
Rcpp, BH, RcppArmadillo
URL
BugReports
https://github.com/osenan/cliqueMS/issues
SystemRequirements
C++11
Encoding
UTF-8
LazyData
true
RoxygenNote
6.0.1
Suggests
knitr, rmarkdown, testthat
VignetteBuilder
knitr
NeedsCompilation
yes
Packaged
2018-05-14 11:16:42 UTC; master
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
Repository
CRAN
Date/Publication
2018-05-14 12:17:36 UTC

install.packages('cliqueMS')

0.2.1

2 months ago

https://github.com/osenan/cliqueMS

Oriol Senan Campos

GPL (>= 2)

Depends on

R (>= 3.4.0)

Imports

Rcpp (>= 0.12.15), xcms, igraph, qlcMatrix, Matrix, CAMERA, methods

Suggests

knitr, rmarkdown, testthat

Discussions