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

## Documentation for package ‘cliqueMS’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

cliqueMS-package | 'cliqueMS' annotates isotopes and adducts in m/z data
anClique | 'anClique' class constructor
anClique-class | 'anClique' S4 class for annotating isotopes and adducts
cliqueMS | 'cliqueMS' annotates isotopes and adducts in m/z data
computeCliques | Computes clique groups from a similarity network
createanClique | 'createanClique' generic function to create an object of class 'anClique'.
createanClique-method | 'createanClique' generic function to create an object of class 'anClique'.
createNetwork | Generic function to create a similarity network from processed m/z data
createNetwork-method | Generic function to create a similarity network from processed m/z data
ex.cliqueGroups | Example m/z processed data
getAnnotation | Annotate adducts and fragments
getCliques | Compute clique groups from processed m/z data
getIsolistanClique | 'anClique' S4 class for annotating isotopes and adducts
getIsolistanClique-method | 'anClique' S4 class for annotating isotopes and adducts
getIsolistanClique<- | 'anClique' S4 class for annotating isotopes and adducts
getIsolistanClique<--method | 'anClique' S4 class for annotating isotopes and adducts
getIsotopes | Annotate isotopes
getlistofCliques | 'anClique' S4 class for annotating isotopes and adducts
getlistofCliques-method | 'anClique' S4 class for annotating isotopes and adducts
getlistofCliques<- | 'anClique' S4 class for annotating isotopes and adducts
getlistofCliques<--method | 'anClique' S4 class for annotating isotopes and adducts
getNetanClique | 'anClique' S4 class for annotating isotopes and adducts
getNetanClique-method | 'anClique' S4 class for annotating isotopes and adducts
getNetanClique<- | 'anClique' S4 class for annotating isotopes and adducts
getNetanClique<--method | 'anClique' S4 class for annotating isotopes and adducts
getPeaklistanClique | 'anClique' S4 class for annotating isotopes and adducts
getPeaklistanClique-method | 'anClique' S4 class for annotating isotopes and adducts
getPeaklistanClique<- | 'anClique' S4 class for annotating isotopes and adducts
getPeaklistanClique<--method | 'anClique' S4 class for annotating isotopes and adducts
hasAnnotation | 'anClique' S4 class for annotating isotopes and adducts
hasAnnotation-method | 'anClique' S4 class for annotating isotopes and adducts
hasAnnotation<- | 'anClique' S4 class for annotating isotopes and adducts
hasAnnotation<--method | 'anClique' S4 class for annotating isotopes and adducts
hasCliques | 'anClique' S4 class for annotating isotopes and adducts
hasCliques-method | 'anClique' S4 class for annotating isotopes and adducts
hasCliques<- | 'anClique' S4 class for annotating isotopes and adducts
hasCliques<--method | 'anClique' S4 class for annotating isotopes and adducts
hasIsotopes | 'anClique' S4 class for annotating isotopes and adducts
hasIsotopes-method | 'anClique' S4 class for annotating isotopes and adducts
hasIsotopes<- | 'anClique' S4 class for annotating isotopes and adducts
hasIsotopes<--method | 'anClique' S4 class for annotating isotopes and adducts
negative.adinfo | Default list of negative charged adducts
positive.adinfo | Default list of positive charged adducts
show-method | 'anClique' S4 class for annotating isotopes and adducts