CAMERA: Collection of annotation related methods for mass spectrometry data
Version 1.32.0

Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments

Browse man pages Browse package API and functions Browse package files

AuthorCarsten Kuhl, Ralf Tautenhahn, Hendrik Treutler, Steffen Neumann {ckuhl|htreutle|sneumann}@ipb-halle.de, rtautenh@scripps.edu
Bioconductor views MassSpectrometry Metabolomics
Date of publicationNone
MaintainerSteffen Neumann <sneumann@ipb-halle.de>
LicenseGPL (>= 2)
Version1.32.0
URL http://msbi.ipb-halle.de/msbi/CAMERA/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CAMERA")

Man pages

annotateDiffreport: Automatic deconvolution/annotation of LC/ESI-MS data
annotate-methods: Automatic deconvolution/annotation of LC/ESI-MS data
calcCaS-methods: EIC correlation grouping of LC/ESI-MS data
calcCiS-methods: Calculate peak distance matrix after EIC correlation
calcIsotopes-methods: Calculate isotope distance matrix from xsAnnotate object
calcPC.hcs-methods: Peakclustering into pseudospectra with the highly connected...
calcPC.lpc-methods: Peakclustering into pseudospectra with the...
calcPC-methods: Peakclustering into pseudospectra according to a distance...
cleanParallel: Cleans up with spawned slave processes after use
combinexsAnnos: Check CAMERA ion species annotation due to matching with...
compoundLibraries: The supported compound databases
compoundQuantiles: compoundQuantiles constructor
compoundQuantiles-class: Class compoundQuantiles encapsulates compound statistics from...
findAdducts-methods: Calculate Adducts and Annotate LC/ESI-MS Spectra
findIsotopes-methods: Deconvolute/Annotate LC/ESI-MS data
findIsotopesWithValidation-methods: 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
getAllPeakEICs-methods: Generate EIC information from raw data
getAtomCount-compoundQuantiles-method: The number of atoms of the given element
getIsotopeCluster: Retrieve the annotatad isotopes
getIsotopeProportion-compoundQuantiles-method: The proportion of the intensities of two isotope peaks
getPeaklist-methods: Generate the annotatad peaklist
getpspectra: Retrieve a peaklist of one or more pseudospectra
groupCorr-methods: EIC correlation grouping of LC/ESI-MS data
groupDen-methods: Density-Grouping of LC/ESI-MS data
groupFWHM-methods: FWHM-Grouping of LC/ESI-MS data
massWindowSizes: The supported mass window sizes
mm14: Extract of marker mixture 14 LC/MS data
plotEIC.xsAnnotate: Plot extracted ion chromatograms from (multiple)...
plotPsSpectrum.xsAnnotate: Plot a Pseudospectrum
psDist-methods: Distance methods for xsAnnotate
pspec2metfrag: Export the putative fragments as MetFrag query files
ruleSet-class: Class 'ruleSet'
xsAnnotate: xsAnnotate constructor for an provided xcmsSet object
xsAnnotate-class: Class xsAnnotate, a class for annotated peak data

Functions

addFragments Source code
add_same_oidscore Source code
annotate Man page
annotate,xcmsSet-method Man page
annotateDiffreport Man page Source code
annotateDiffreport,xsAnnotate-methods Man page
annotateGrp Source code
annotateGrpMPI Source code
annotateGrpMPI2 Source code
calcCL Source code
calcCL3 Source code
calcCaS Man page
calcCaS,xsAnnotate-method Man page
calcCiS Man page
calcCiS,xsAnnotate-method Man page
calcIsotopeMatrix Source code
calcIsotopes Man page
calcIsotopes,xsAnnotate-method Man page
calcPC Man page
calcPC,calcPC-method Man page
calcPC,xsAnnotate-method Man page
calcPC.hcs Man page
calcPC.hcs,xsAnnotate-method Man page
calcPC.lpc Man page
calcPC.lpc,xsAnnotate-method Man page
calcRules Source code
checkHypothese Source code
checkIps Source code
checkIsotopes Source code
checkOidCausality Source code
checkQuasimolion Source code
class:ruleSet Man page
cleanParallel Man page Source code
combineHypothese Source code
combinexsAnnos Man page Source code
compoundLibraries Man page Source code
compoundQuantiles Man page Source code
compoundQuantiles-class Man page
create.matrix Source code
createHypothese Source code
example Source code
extractfragments Source code
fastMatch Source code
fast_corr Source code
findAdducts Man page
findAdducts,xsAnnotate-method Man page
findIsotopes Man page
findIsotopes,xsAnnotate-method Man page
findIsotopesForPS Source code
findIsotopesPspec Source code
findIsotopesWithValidation Man page
findIsotopesWithValidation,xsAnnotate-method Man page
findKendrickMasses Man page Source code
findNeutralLoss Man page Source code
findNeutralLossSpecs Man page Source code
fragments2metfrag Source code
fragments2metfusion Source code
generateRules Man page
generateRules,ruleSet-method Man page
getAllEICs Source code
getAllPeakEICs Man page
getAllPeakEICs,xsAnnotate-method Man page
getAtomCount Man page
getAtomCount,compoundQuantiles-method Man page
getEIC Source code
getEIC4Peaks Source code
getEICs Source code
getIsotopeCluster Man page Source code
getIsotopeProportion Man page
getIsotopeProportion,compoundQuantiles-method Man page
getMaxScans Source code
getPeaklist Man page
getPeaklist,xsAnnotate-method Man page
getPeaks Source code
getPeaksIdxCol Source code
getPeaks_selection Source code
getderivativeIons Source code Source code
getpspectra Man page Source code
groupCorr Man page
groupCorr,xsAnnotate-method Man page
groupDen Man page
groupDen,xsAnnotate-method Man page
groupFWHM Man page
groupFWHM,xsAnnotate-method Man page
is.wholenumber Source code
massDiffMatrix Source code
massDiffMatrixNL Source code
massWindowSizes Man page Source code
mm14 Man page
msgfun.snowParallel Source code
naOmit Source code
onLoad Source code
percentOutput Source code
plotEICs Man page
plotEICs,xsAnnotate-method Man page
plotEICs.xsAnnotate Man page
plotPsSpectrum Man page
plotPsSpectrum,xsAnnotate-method Man page
plotPsSpectrum.xsAnnotate Man page
psDist Man page
psDist,CAMERA-method Man page
psDist-methods Man page
pspec2metfrag Man page Source code
pspec2metfusion Man page Source code
readLists Man page
readLists,ruleSet-method Man page
resolveFragmentConnections Source code
ruleSet-class Man page
setCAMERAOptions Source code
setDefaultLists Man page
setDefaultLists,ruleSet-method Man page
setDefaultParams Man page
setDefaultParams,ruleSet-method Man page
setParams Man page
setParams,ruleSet,numeric,numeric,numeric,numeric,numeric,numeri Man page
show,ruleSet-method Man page
show,xsAnnotate-method Man page
xsAnnotate Man page Source code
xsAnnotate-class Man page

Files

.travis.yml
DESCRIPTION
NAMESPACE
R
R/00xsAnnotate.R
R/compoundQuantiles.R
R/fastMatch.R
R/fct_findAdducts.R
R/fct_findIsotopes.R
R/fct_findIsotopesWithValidation.R
R/fct_groupCorr.R
R/init.R
R/psDist.R
R/pspec2metfrag.R
R/ruleSet.R
R/unix
R/windows
R/xsAnnotate.R
R/xsVisualise.R
R/zzz.R
README.md
build
build/vignette.rds
data
data/mm14.rda
inst
inst/CITATION
inst/NEWS
inst/ONEWS
inst/doc
inst/doc/CAMERA.R
inst/doc/CAMERA.Rnw
inst/doc/CAMERA.pdf
inst/doc/IsotopeDetectionVignette.Rnw
inst/doc/IsotopeDetectionVignette.pdf
inst/doc/compoundQuantilesVignette.Rnw
inst/doc/compoundQuantilesVignette.pdf
inst/lists
inst/lists/ions.csv
inst/lists/neutraladdition.csv
inst/lists/neutralloss.csv
inst/mzdata
inst/mzdata/MM14.mzdata
inst/quantiles
inst/quantiles/lib_LipidMaps__maxDa_500
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/Br_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/C_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/Cl_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/F_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/H_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/I_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/IsotopeQuantiles__iso_1.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/IsotopeQuantiles__iso_2.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/IsotopeQuantiles__iso_3.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/IsotopeQuantiles__iso_4.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/IsotopeQuantiles__iso_5.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/N_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/O_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/P_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/S_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/Si_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/Unknown_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/Br_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/C_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/Cl_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/F_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/H_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/I_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/IsotopeQuantiles__iso_1.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/IsotopeQuantiles__iso_2.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/IsotopeQuantiles__iso_3.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/IsotopeQuantiles__iso_4.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/IsotopeQuantiles__iso_5.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/N_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/O_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/P_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/S_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/Si_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/Unknown_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/Br_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/C_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/Cl_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/F_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/H_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/I_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/IsotopeQuantiles__iso_1.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/IsotopeQuantiles__iso_2.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/IsotopeQuantiles__iso_3.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/IsotopeQuantiles__iso_4.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/IsotopeQuantiles__iso_5.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/N_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/O_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/P_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/S_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/Si_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/Unknown_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/Br_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/C_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/Cl_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/F_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/H_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/I_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/IsotopeQuantiles__iso_1.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/IsotopeQuantiles__iso_2.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/IsotopeQuantiles__iso_3.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/IsotopeQuantiles__iso_4.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/IsotopeQuantiles__iso_5.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/N_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/O_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/P_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/S_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/Si_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/Unknown_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/Br_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/C_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/Cl_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/F_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/H_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/I_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/IsotopeQuantiles__iso_1.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/IsotopeQuantiles__iso_2.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/IsotopeQuantiles__iso_3.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/IsotopeQuantiles__iso_4.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/IsotopeQuantiles__iso_5.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/N_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/O_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/P_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/S_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/Si_quantiles.tsv
inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/Unknown_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/Br_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/C_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/Cl_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/F_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/H_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/I_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/IsotopeQuantiles__iso_1.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/IsotopeQuantiles__iso_2.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/IsotopeQuantiles__iso_3.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/IsotopeQuantiles__iso_4.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/IsotopeQuantiles__iso_5.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/N_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/O_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/P_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/S_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/Si_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/Unknown_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/Br_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/C_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/Cl_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/F_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/H_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/I_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/IsotopeQuantiles__iso_1.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/IsotopeQuantiles__iso_2.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/IsotopeQuantiles__iso_3.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/IsotopeQuantiles__iso_4.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/IsotopeQuantiles__iso_5.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/N_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/O_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/P_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/S_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/Si_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/Unknown_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/Br_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/C_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/Cl_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/F_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/H_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/I_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/IsotopeQuantiles__iso_1.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/IsotopeQuantiles__iso_2.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/IsotopeQuantiles__iso_3.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/IsotopeQuantiles__iso_4.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/IsotopeQuantiles__iso_5.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/N_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/O_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/P_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/S_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/Si_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/Unknown_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/Br_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/C_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/Cl_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/F_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/H_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/I_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/IsotopeQuantiles__iso_1.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/IsotopeQuantiles__iso_2.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/IsotopeQuantiles__iso_3.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/IsotopeQuantiles__iso_4.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/IsotopeQuantiles__iso_5.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/N_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/O_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/P_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/S_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/Si_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/Unknown_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/Br_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/C_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/Cl_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/F_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/H_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/I_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/IsotopeQuantiles__iso_1.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/IsotopeQuantiles__iso_2.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/IsotopeQuantiles__iso_3.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/IsotopeQuantiles__iso_4.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/IsotopeQuantiles__iso_5.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/N_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/O_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/P_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/S_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/Si_quantiles.tsv
inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/Unknown_quantiles.tsv
inst/quantiles/lib_kegg__maxDa_1000
inst/quantiles/lib_kegg__maxDa_1000/windowSize_10
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inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/P_quantiles.tsv
inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/S_quantiles.tsv
inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/Si_quantiles.tsv
inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/Unknown_quantiles.tsv
inst/rules
inst/rules/extended_adducts_neg.csv
inst/rules/extended_adducts_pos.csv
inst/rules/primary_adducts_neg.csv
inst/rules/primary_adducts_pos.csv
inst/unitTests
inst/unitTests/Makefile
inst/unitTests/test_annotateDiffreport.R
inst/unitTests/test_compoundQuantiles.R
inst/unitTests/test_findAdductsMPI.R
inst/unitTests/test_generateRules.R
inst/unitTests/test_groupCorr.R
inst/unitTests/test_groupFWHM.R
inst/unitTests/test_kendrick.R
inst/unitTests/test_psDist.R
inst/unitTests/test_pspec2metfrag.R
man
man/annotate-methods.Rd
man/annotateDiffreport.Rd
man/calcCaS-methods.Rd
man/calcCiS-methods.Rd
man/calcIsotopes-methods.Rd
man/calcPC-methods.Rd
man/calcPC.hcs-methods.Rd
man/calcPC.lpc-methods.Rd
man/cleanParallel.Rd
man/combinexsAnnos.Rd
man/compoundLibraries.Rd
man/compoundQuantiles-class.Rd
man/compoundQuantiles.Rd
man/findAdducts-methods.Rd
man/findIsotopes-methods.Rd
man/findIsotopesWithValidation-methods.Rd
man/findKendrickMasses.Rd
man/findNeutralLoss.Rd
man/findNeutralLossSpecs.Rd
man/getAllPeakEICs-methods.Rd
man/getAtomCount-compoundQuantiles-method.Rd
man/getIsotopeCluster.Rd
man/getIsotopeProportion-compoundQuantiles-method.Rd
man/getPeaklist-methods.Rd
man/getpspectra.Rd
man/groupCorr-methods.Rd
man/groupDen-methods.Rd
man/groupFWHM-methods.Rd
man/massWindowSizes.Rd
man/mm14.Rd
man/plotEIC.xsAnnotate.Rd
man/plotPsSpectrum.xsAnnotate.Rd
man/psDist-methods.Rd
man/pspec2metfrag.Rd
man/ruleSet-class.Rd
man/xsAnnotate-class.Rd
man/xsAnnotate.Rd
src
src/fastMatch.c
tests
tests/runTests.R
vignettes
vignettes/CAMERA.Rnw
vignettes/IsotopeDetectionVignette.Rnw
vignettes/compoundQuantilesVignette.Rnw
CAMERA documentation built on May 20, 2017, 9:33 p.m.