Collection of annotation related methods for mass spectrometry data

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Documentation for package ‘CAMERA’ version 1.44.0

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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