Package: cliqueMS 1.27.0

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_1.27.0.tar.gz
cliqueMS_1.27.0.zip(r-4.7)cliqueMS_1.27.0.zip(r-4.6)
cliqueMS_1.27.0.tgz(r-4.6-x86_64)cliqueMS_1.27.0.tgz(r-4.6-arm64)
cliqueMS_1.27.0.tar.gz(r-4.7-arm64)cliqueMS_1.27.0.tar.gz(r-4.7-x86_64)cliqueMS_1.27.0.tar.gz(r-4.6-arm64)cliqueMS_1.27.0.tar.gz(r-4.6-x86_64)
cliqueMS_1.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cliqueMS/json (API)

# Install 'cliqueMS' in R:

install.packages('cliqueMS', repos = c('https://bioc.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:

ex.cliqueGroups - Example m/z processed data
negative.adinfo - Default list of negative charged adducts
positive.adinfo - Default list of positive charged adducts

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

metabolomics massspectrometry network networkinference cpp

6.52 score 13 stars 28 scripts 3 mentions 20 exports 138 dependencies

Last updated from:e8acd497ac. Checks:3 WARNING, 6 NOTE, 2 OK, 3 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	234
linux-devel-arm64	NOTE	438
linux-devel-x86_64	NOTE	513
source / vignettes	OK	339
linux-release-arm64	NOTE	420
linux-release-x86_64	NOTE	524
macos-release-arm64	WARNING	279
macos-release-x86_64	WARNING	454
macos-oldrel-arm64	FAIL	75
macos-oldrel-x86_64	FAIL	157
windows-devel	NOTE	494
windows-release	NOTE	512
windows-oldrel	FAIL	120
wasm-release	OK	214

Exports:computeCliques createanClique createNetwork getAnnotation getCliques getIsolistanClique getIsotopes getlistofCliques getlistofCliques<-getNetanClique getNetanClique<-getPeaklistanClique getPeaklistanClique<-hasAnnotation hasAnnotation<-hasCliques hasCliques<-hasIsotopes hasIsotopes<-show

Dependencies:abind affy affyio AnnotationFilter askpass base64enc BH Biobase BiocBaseUtils BiocGenerics biocmake BiocManager BiocParallel bslib cachem cli clue cluster codetools coop cpp11 crayon crosstalk curl data.table DBI DelayedArray digest dir.expiry doParallel dplyr evaluate farver fastmap filelock fontawesome foreach formatR fs futile.logger futile.options generics GenomicRanges ggplot2 glue gtable highr hms htmltools htmlwidgets httr igraph impute IRanges isoband iterators jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle limma magrittr MALDIquant MASS MassSpecWavelet Matrix MatrixGenerics matrixStats memoise MetaboCoreUtils mime MsCoreUtils MsExperiment MsFeatures MSnbase MultiAssayExperiment mzID mzR ncdf4 openssl otel pcaMethods pillar pkgconfig plotly plyr preprocessCore prettyunits progress promises ProtGenerics PSMatch PTMods purrr QFeatures R6 rappdirs RColorBrewer Rcpp RcppArmadillo reshape2 Rhdf5lib rlang rmarkdown S4Arrays S4Vectors S7 sass scales Seqinfo slam snow SparseArray Spectra statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite vsn withr xcms xfun XML XVector yaml

Annotating LC/MS data with cliqueMS

Rendered fromannotate_features.Rmdusingknitr::rmarkdown

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

Help page	Topics
'anClique' class constructor	anClique
'anClique' S4 class for annotating isotopes and adducts	anClique-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 data	cliqueMS-package cliqueMS
Computes clique groups from a similarity network	computeCliques
'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 data	createNetwork createNetwork,XCMSnExp-method createNetwork,xcmsSet-method
Example m/z processed data	ex.cliqueGroups
Annotate adducts and fragments	getAnnotation
Compute clique groups from processed m/z data	getCliques
Annotate isotopes	getIsotopes
Default list of negative charged adducts	negative.adinfo
Default list of positive charged adducts	positive.adinfo

Package: cliqueMS 1.27.0

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

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