# Collection of annotation related methods for mass spectrometry data

## Documentation for package ‘CAMERA’ version 1.60.0

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

## Help Pages

annotate | Automatic deconvolution/annotation of LC/ESI-MS data
annotate-method | Automatic deconvolution/annotation of LC/ESI-MS data
annotateDiffreport | Automatic deconvolution/annotation of LC/ESI-MS data
annotateDiffreport,xsAnnotate-methods | Automatic deconvolution/annotation of LC/ESI-MS data
calcCaS | EIC correlation grouping of LC/ESI-MS data
calcCaS-method | EIC correlation grouping of LC/ESI-MS data
calcCiS | Calculate peak distance matrix after EIC correlation
calcCiS-method | Calculate peak distance matrix after EIC correlation
calcIsotopes | Calculate isotope distance matrix from xsAnnotate object
calcIsotopes-method | Calculate isotope distance matrix from xsAnnotate object
calcPC | Peakclustering into pseudospectra according to a distance matrix
calcPC-method | Peakclustering into pseudospectra according to a distance matrix
calcPC.hcs | Peakclustering into pseudospectra with the highly connected subgraphs approach
calcPC.hcs-method | Peakclustering into pseudospectra with the highly connected subgraphs approach
calcPC.lpc | Peakclustering into pseudospectra with the label-propagation-community algorithm
calcPC.lpc-method | Peakclustering into pseudospectra with the label-propagation-community algorithm
class:ruleSet | Class 'ruleSet'
cleanParallel | Cleans up with spawned slave processes after use
combinexsAnnos | Check CAMERA ion species annotation due to matching with opposite ion mode
compoundLibraries | The supported compound databases
compoundQuantiles | compoundQuantiles constructor
compoundQuantiles-class | Class compoundQuantiles encapsulates compound statistics from different databases.
findAdducts | Calculate Adducts and Annotate LC/ESI-MS Spectra
findAdducts-method | Calculate Adducts and Annotate LC/ESI-MS Spectra
findIsotopes | Deconvolute/Annotate LC/ESI-MS data
findIsotopes-method | Deconvolute/Annotate LC/ESI-MS data
findIsotopesWithValidation | Deconvolute/Annotate LC/ESI-MS data
findIsotopesWithValidation-method | Deconvolute/Annotate LC/ESI-MS data
findKendrickMasses | Find specfic mass defects using Kendrick mass scales
findNeutralLoss | Find pseudospectra that contains a specific neutral loss
findNeutralLossSpecs | Find pseudospectra that contains a specific neutral loss
generateRules | Class 'ruleSet'
generateRules-method | Class 'ruleSet'
getAllPeakEICs | Generate EIC information from raw data
getAllPeakEICs-method | Generate EIC information from raw data
getAtomCount | The number of atoms of the given element
getAtomCount-method | The number of atoms of the given element
getIsotopeCluster | Retrieve the annotatad isotopes
getIsotopeProportion | The proportion of the intensities of two isotope peaks
getIsotopeProportion-method | The proportion of the intensities of two isotope peaks
getPeaklist | Generate the annotatad peaklist
getPeaklist-method | Generate the annotatad peaklist
getpspectra | Retrieve a peaklist of one or more pseudospectra
getReducedPeaklist | Generate reduced peaklist from the annotatad peaklist
getReducedPeaklist-method | Generate reduced peaklist from the annotatad peaklist
groupCorr | EIC correlation grouping of LC/ESI-MS data
groupCorr-method | EIC correlation grouping of LC/ESI-MS data
groupDen | Density-Grouping of LC/ESI-MS data
groupDen-method | Density-Grouping of LC/ESI-MS data
groupFWHM | FWHM-Grouping of LC/ESI-MS data
groupFWHM-method | FWHM-Grouping of LC/ESI-MS data
massWindowSizes | The supported mass window sizes
mm14 | Extract of marker mixture 14 LC/MS data
plotEICs | Plot extracted ion chromatograms from (multiple) Pseudospectra
plotEICs-method | Plot extracted ion chromatograms from (multiple) Pseudospectra
plotEICs.xsAnnotate | Plot extracted ion chromatograms from (multiple) Pseudospectra
plotPsSpectrum | Plot a Pseudospectrum
plotPsSpectrum-method | Plot a Pseudospectrum
plotPsSpectrum.xsAnnotate | Plot a Pseudospectrum
psDist | Distance methods for xsAnnotate
psDist-method | Distance methods for xsAnnotate
psDist-methods | Distance methods for xsAnnotate
pspec2metfrag | Export the putative fragments as MetFrag query files
pspec2metfusion | Export the putative fragments as MetFrag query files
readLists | Class 'ruleSet'
readLists-method | Class 'ruleSet'
ruleSet-class | Class 'ruleSet'
setDefaultLists | Class 'ruleSet'
setDefaultLists-method | Class 'ruleSet'
setDefaultParams | Class 'ruleSet'
setDefaultParams-method | Class 'ruleSet'
setParams | Class 'ruleSet'
setParams-method | Class 'ruleSet'
show-method | Class 'ruleSet'
show-method | Class xsAnnotate, a class for annotated peak data
xsAnnotate | xsAnnotate constructor for an provided xcmsSet object
xsAnnotate-class | Class xsAnnotate, a class for annotated peak data