Collection of annotation related methods for mass spectrometry data


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Documentation for package ‘CAMERA’ version 1.12.0

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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
cleanParallel Cleans up with spawned slave processes after use
combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode
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
findNeutralLoss Find pseudospectra that contains a specific neutral loss
findNeutralLossSpecs Find pseudospectra that contains a specific neutral loss
getAllPeakEICs Generate EIC information from raw data
getAllPeakEICs-method Generate EIC information from raw data
getIsotopeCluster Retrieve the annotatad isotopes
getPeaklist Generate the annotatad peaklist
getPeaklist-method Generate the annotatad peaklist
getpspectra Retrieve a peaklist of one or more pseudospectra
groupCorr EIC correlation grouping of LC/ESI-MS data
groupCorr-method EIC correlation grouping of LC/ESI-MS data
groupFWHM FWHM-Grouping of LC/ESI-MS data
groupFWHM-method FWHM-Grouping of LC/ESI-MS data
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
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