CAMERA: Collection of annotation related methods for mass spectrometry data

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

AuthorCarsten Kuhl, Ralf Tautenhahn, Hendrik Treutler, Steffen Neumann {ckuhl|htreutle|sneumann}@ipb-halle.de, rtautenh@scripps.edu
Date of publicationNone
MaintainerSteffen Neumann <sneumann@ipb-halle.de>
LicenseGPL (>= 2)
Version1.30.0
http://msbi.ipb-halle.de/msbi/CAMERA/

View on Bioconductor

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

Files in this package

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

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