Package: MetaboAnnotation 1.11.0

Johannes Rainer

MetaboAnnotation: Utilities for Annotation of Metabolomics Data

High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on mass matching but also functions to consider m/z and retention times for annotation of LC-MS features given that respective reference values are available. In addition, the function provides high-level functions to simplify matching of LC-MS/MS spectra against spectral libraries and objects and functionality to represent and manage such matched data.

Authors:Michael Witting [aut], Johannes Rainer [aut, cre], Andrea Vicini [aut], Carolin Huber [aut], Philippine Louail [aut], Nir Shachaf [ctb]

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MetaboAnnotation.pdf |MetaboAnnotation.html✨
MetaboAnnotation/json (API)
NEWS

# Install 'MetaboAnnotation' in R:
install.packages('MetaboAnnotation', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/rformassspectrometry/metaboannotation/issues

On BioConductor:MetaboAnnotation-1.9.2(bioc 3.20)MetaboAnnotation-1.8.1(bioc 3.19)

infrastructuremetabolomicsmassspectrometryannotationmass-spectromtry

6.98 score 15 stars 30 scripts 504 downloads 46 exports 135 dependencies

Last updated 23 days agofrom:4a21c91d87. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:addMatchesaddProcessingcolnamesCompareSpectraParamCompDbSourcecreateStandardMixesendoapplyfilterMatcheslapplyMass2MzParamMass2MzRtParamMassBankSourceMatchedmatchedDataMatchedSpectramatchesmatchFormulaMatchForwardReverseParammatchMzmatchSpectramatchValuesmetadataMz2MassParamMz2MassRtParamMzParamMzRtParamplotSpectraMirrorpruneTargetqueryqueryIndexqueryVariablesScoreThresholdParamscoreVariablesSelectMatchesParamsetBackendshowSingleMatchParamspectraVariablestargettargetIndextargetVariablesTopRankedMatchesParamvalidateMatchedSpectraValueParamwhichQuerywhichTarget

Dependencies:abindAnnotationDbiAnnotationFilterAnnotationHubaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobbslibcachemChemmineRcliclueclustercodetoolscolorspaceCompoundDbcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydigestdplyrDTevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmgcvmimeMsCoreUtilsMultiAssayExperimentmunsellnlmeopensslpillarpkgconfigplogrplotlyplyrpngpromisesProtGenericspurrrQFeaturesR6rappdirsRColorBrewerRcppRCurlreshape2rjsonrlangrmarkdownRSQLitersvgS4ArraysS4VectorssassscalessnowSparseArraySpectrastringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunxml2XVectoryamlzlibbioc

Annotation of MS-based Metabolomics Data

Rendered fromMetaboAnnotation.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-04-29
Started: 2021-03-24

Readme and manuals

Help Manual

Help pageTopics
Representation of generic objects matches$,Matched-method addMatches addMatches,Matched-method colnames,Matched-method endoapply endoapply,ANY-method endoapply,Matched-method filterMatches filterMatches,Matched,missing-method filterMatches,Matched,ScoreThresholdParam-method filterMatches,Matched,SelectMatchesParam-method filterMatches,Matched,SingleMatchParam-method filterMatches,Matched,TopRankedMatchesParam-method lapply,Matched-method length,Matched-method Matched Matched-class matchedData matchedData,Matched-method matches pruneTarget query,Matched-method queryIndex queryVariables queryVariables,Matched-method ScoreThresholdParam scoreVariables SelectMatchesParam show,Matched-method SingleMatchParam target targetIndex targetVariables targetVariables,Matched-method TopRankedMatchesParam whichQuery whichTarget [,Matched,ANY,ANY,ANY-method [,Matched-method
Compound Annotation SourcesCompAnnotationSource CompAnnotationSource-class matchSpectra,Spectra,CompAnnotationSource,Param-method metadata,CompAnnotationSource-method show,CompAnnotationSource-method
Compound Annotation Sources for 'CompDb' databasesCompDbSource CompDbSource-class MassBankSource metadata,CompDbSource-method show,CompDbSource-method
Create Standard Mixes from a Matrix of Standard CompoundscreateStandardMixes
Representation of Spectra matches$,MatchedSpectra-method addProcessing,MatchedSpectra-method colnames,MatchedSpectra-method matchedData,MatchedSpectra-method MatchedSpectra MatchedSpectra-class plotSpectraMirror,MatchedSpectra-method queryVariables,MatchedSpectra-method setBackend,MatchedSpectra,MsBackend-method spectraData,MatchedSpectra-method spectraVariables,MatchedSpectra-method targetVariables,MatchedSpectra-method
Chemical Formula MatchingmatchFormula matchFormula,character,character-method matchFormula,character,data.frameOrSimilar-method matchFormula,data.frameOrSimilar,character-method matchFormula,data.frameOrSimilar,data.frameOrSimilar-method
Spectral matchingmatchSpectra
Matching MS Spectra against a referenceCompareSpectraParam CompareSpectraParam-class MatchForwardReverseParam MatchForwardReverseParam-class matchSpectra,Spectra,CompDb,Param-method matchSpectra,Spectra,CompDbSource,Param-method matchSpectra,Spectra,Spectra,CompareSpectraParam-method matchSpectra,Spectra,Spectra,MatchForwardReverseParam-method
Validating MatchedSpectravalidateMatchedSpectra
Matching of numeric valuesMass2MzParam Mass2MzRtParam matchMz matchValues matchValues,data.frameOrSimilar,data.frameOrSimilar,Mass2MzParam-method matchValues,data.frameOrSimilar,data.frameOrSimilar,Mass2MzRtParam-method matchValues,data.frameOrSimilar,data.frameOrSimilar,Mz2MassParam-method matchValues,data.frameOrSimilar,data.frameOrSimilar,Mz2MassRtParam-method matchValues,data.frameOrSimilar,data.frameOrSimilar,MzParam-method matchValues,data.frameOrSimilar,data.frameOrSimilar,MzRtParam-method matchValues,data.frameOrSimilar,data.frameOrSimilar,ValueParam-method matchValues,data.frameOrSimilar,numeric,Mass2MzParam-method matchValues,data.frameOrSimilar,numeric,Mz2MassParam-method matchValues,data.frameOrSimilar,numeric,MzParam-method matchValues,data.frameOrSimilar,numeric,ValueParam-method matchValues,data.frameOrSimilar,Spectra,MzParam-method matchValues,data.frameOrSimilar,Spectra,MzRtParam-method matchValues,numeric,data.frameOrSimilar,Mass2MzParam-method matchValues,numeric,data.frameOrSimilar,Mz2MassParam-method matchValues,numeric,data.frameOrSimilar,MzParam-method matchValues,numeric,data.frameOrSimilar,ValueParam-method matchValues,numeric,numeric,Mass2MzParam-method matchValues,numeric,numeric,Mz2MassParam-method matchValues,numeric,numeric,ValueParam-method matchValues,numeric,Spectra,MzParam-method Mz2MassParam Mz2MassRtParam MzParam MzRtParam ValueParam