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

## Documentation for package ‘cliqueMS’ version 0.3.1

- 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' for annotating isotopes and adducts
anClique-class | 'anClique-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.XCMSnExp | 'createanClique.XCMSnExp' produces an object of class 'anClique'.
createanClique.xcmsSet | 'createanClique.xcmsSet' produces an object of class 'anClique'.
createNetwork | Generic function to create a similarity network from processed m/z data
createNetwork.XCMSnExp | Function to create a similarity network from 'XCMSnExp' processed m/z data
createNetwork.xcmsSet | Function to create a similarity network from 'xcmsSet' 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
getIsotopes | Annotate isotopes
negative.adinfo | Default list of negative charged adducts
positive.adinfo | Default list of positive charged adducts