Package: MetaboAnnotation 1.9.1

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'))

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

On BioConductor:MetaboAnnotation-1.9.1(bioc 3.20)MetaboAnnotation-1.8.1(bioc 3.19)

bioconductor-package

46 exports 1.58 score 135 dependencies

Last updated 2 months agofrom:b96137d03b

Exports:addMatches addProcessing colnames CompareSpectraParam CompDbSource createStandardMixes endoapply filterMatches lapply Mass2MzParam Mass2MzRtParam MassBankSource Matched matchedData MatchedSpectra matches matchFormula MatchForwardReverseParam matchMz matchSpectra matchValues metadata Mz2MassParam Mz2MassRtParam MzParam MzRtParam plotSpectraMirror pruneTarget query queryIndex queryVariables ScoreThresholdParam scoreVariables SelectMatchesParam setBackend show SingleMatchParam spectraVariables target targetIndex targetVariables TopRankedMatchesParam validateMatchedSpectra ValueParam whichQuery whichTarget

Dependencies:abind AnnotationDbi AnnotationFilter AnnotationHub askpass base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob bslib cachem ChemmineR cli clue cluster codetools colorspace CompoundDb cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray digest dplyr DT evaluate fansi farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gridExtra gtable highr htmltools htmlwidgets httpuv httr igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise MetaboCoreUtils mgcv mime MsCoreUtils MultiAssayExperiment munsell nlme openssl pillar pkgconfig plogr plotly plyr png promises ProtGenerics purrr QFeatures R6 rappdirs RColorBrewer Rcpp RCurl reshape2 rjson rlang rmarkdown RSQLite rsvg S4Arrays S4Vectors sass scales snow SparseArray Spectra stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun xml2 XVector yaml zlibbioc

Annotation of MS-based Metabolomics Data

Rendered fromMetaboAnnotation.Rmdusingknitr::rmarkdownon Jun 16 2024.

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

Help page	Topics
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 Sources	CompAnnotationSource CompAnnotationSource-class matchSpectra,Spectra,CompAnnotationSource,Param-method metadata,CompAnnotationSource-method show,CompAnnotationSource-method
Compound Annotation Sources for 'CompDb' databases	CompDbSource CompDbSource-class MassBankSource metadata,CompDbSource-method show,CompDbSource-method
Create Standard Mixes from a Matrix of Standard Compounds	createStandardMixes
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 Matching	matchFormula matchFormula,character,character-method matchFormula,character,data.frameOrSimilar-method matchFormula,data.frameOrSimilar,character-method matchFormula,data.frameOrSimilar,data.frameOrSimilar-method
Spectral matching	matchSpectra
Matching MS Spectra against a reference	CompareSpectraParam 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 MatchedSpectra	validateMatchedSpectra
Matching of numeric values	Mass2MzParam 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

Package: MetaboAnnotation 1.9.1

MetaboAnnotation: Utilities for Annotation of Metabolomics Data

Annotation of MS-based Metabolomics Data

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