Package: cliqueMS 1.26.0

Oriol Senan Campos

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, Bioinformatics, 35(20), 2019), '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.

Authors:Oriol Senan Campos [aut, cre], Antoni Aguilar-Mogas [aut], Jordi Capellades [aut], Miriam Navarro [aut], Oscar Yanes [aut], Roger Guimera [aut], Marta Sales-Pardo [aut]

cliqueMS_1.26.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
cliqueMS/json (API)
NEWS

# Install 'cliqueMS' in R:
install.packages('cliqueMS', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/osenan/cliquems/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:cliqueMS-1.27.0(bioc 3.24)cliqueMS-1.26.0(bioc 3.23)

metabolomicsmassspectrometrynetworknetworkinferencecpp

6.46 score 12 stars 27 scripts 412 downloads 3 mentions 20 exports 138 dependencies

Last updated from:c65c5dbea6 (on RELEASE_3_23). Checks:7 NOTE, 2 OK, 2 WARNING, 3 FAIL. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE247
linux-devel-arm64NOTE442
linux-devel-x86_64NOTE525
source / vignettesOK458
linux-release-arm64NOTE428
linux-release-x86_64NOTE587
macos-release-arm64WARNING301
macos-release-x86_64WARNING580
macos-oldrel-arm64FAIL191
macos-oldrel-x86_64FAIL212
windows-develNOTE647
windows-releaseNOTE552
windows-oldrelFAIL412
wasm-releaseOK194

Exports:computeCliquescreateanCliquecreateNetworkgetAnnotationgetCliquesgetIsolistanCliquegetIsotopesgetlistofCliquesgetlistofCliques<-getNetanCliquegetNetanClique<-getPeaklistanCliquegetPeaklistanClique<-hasAnnotationhasAnnotation<-hasCliqueshasCliques<-hasIsotopeshasIsotopes<-show

Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsbiocmakeBiocManagerBiocParallelbslibcachemcliclueclustercodetoolscoopcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdir.expirydoParalleldplyrevaluatefarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmzIDmzRncdf4opensslotelpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchPTModspurrrQFeaturesR6rappdirsRColorBrewerRcppRcppArmadilloreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfoslamsnowSparseArraySpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitevsnwithrxcmsxfunXMLXVectoryaml

Annotating LC/MS data with cliqueMS

Oriol Senan

Rendered fromannotate_features.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2024-08-03
Started: 2018-03-22

Readme and manuals

Help Manual

Help pageTopics
'anClique' class constructoranClique
'anClique' S4 class for annotating isotopes and adductsanClique-class getIsolistanClique getIsolistanClique,anClique-method getIsolistanClique<- getIsolistanClique<-,anClique-method getlistofCliques getlistofCliques,anClique-method getlistofCliques<- getlistofCliques<-,anClique-method getNetanClique getNetanClique,anClique-method getNetanClique<- getNetanClique<-,anClique-method getPeaklistanClique getPeaklistanClique,anClique-method getPeaklistanClique<- getPeaklistanClique<-,anClique-method hasAnnotation hasAnnotation,anClique-method hasAnnotation<- hasAnnotation<-,anClique-method hasCliques hasCliques,anClique-method hasCliques<- hasCliques<-,anClique-method hasIsotopes hasIsotopes,anClique-method hasIsotopes<- hasIsotopes<-,anClique-method show,anClique-method
'cliqueMS' annotates isotopes and adducts in m/z datacliqueMS-package cliqueMS
Computes clique groups from a similarity networkcomputeCliques
'createanClique' generic function to create an object of class 'anClique'.createanClique createanClique,XCMSnExp-method createanClique,xcmsSet-method
Generic function to create a similarity network from processed m/z datacreateNetwork createNetwork,XCMSnExp-method createNetwork,xcmsSet-method
Example m/z processed dataex.cliqueGroups
Annotate adducts and fragmentsgetAnnotation
Compute clique groups from processed m/z datagetCliques
Annotate isotopesgetIsotopes
Default list of negative charged adductsnegative.adinfo
Default list of positive charged adductspositive.adinfo