Package: metaMS 1.49.0

Yann Guitton

metaMS: MS-based metabolomics annotation pipeline

MS-based metabolomics data processing and compound annotation pipeline.

Authors:Ron Wehrens [aut], Pietro Franceschi [aut], Nir Shahaf [ctb], Matthias Scholz [ctb], Georg Weingart [ctb], Elisabete Carvalho [ctb], Yann Guitton [ctb, cre], Julien Saint-Vanne [ctb]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
metaMS/json (API)

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

Bug tracker:https://github.com/yguitton/metams/issues

Datasets:
  • DB - Information on three chemical standards measured in GC-MS
  • errf - Mass error surface for Waters Synapt Q-TOF spectrometers
  • exptable - Sample table for the generation of a database of standards
  • GCresults - Results of metaMS for a small GC-MS data set
  • LCDBtest - Sample DB for LC-MS annotation
  • LCresults - Result metaMS for a small LC-MS data set
  • Orbitrap.RP - Example settings for 'metaMS'
  • smallDB - Information on three chemical standards measured in GC-MS
  • stdInfo - Information on three chemical standards measured in GC-MS
  • Synapt.NP - Example settings for 'metaMS'
  • Synapt.RP - Example settings for 'metaMS'
  • TSQXLS.GC - Example settings for 'metaMS'

On BioConductor:metaMS-1.49.0(bioc 3.24)metaMS-1.48.0(bioc 3.23)

immunooncologymassspectrometrymetabolomics

7.53 score 15 stars 16 scripts 13 mentions 33 exports 151 dependencies

Last updated from:f0d1d142aa. Checks:8 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING233
linux-devel-x86_64WARNING530
source / vignettesOK388
linux-release-x86_64WARNING485
macos-release-arm64WARNING383
macos-oldrel-arm64WARNING318
windows-develWARNING407
windows-releaseWARNING402
windows-oldrelWARNING389
wasm-releaseOK220

Exports:addRIalignmentLCAnnotateFeatureAnnotateTableconstruct.mspconstructExpPseudoSpectracreateSTDdbGCcreateSTDdbLCfilter.mspgenerateStdDBGCgenerateStdDBLCgetAnnotationLCgetAnnotationMatgetFeatureInfogetPeakTablematchExpSpecmatchSamples2DBmatchSamples2SamplesmetaMSsettingsmetaSettingmetaSetting<-peakDetectionplotPseudoSpectrumprocessStandardsread.mspreadStdInforunCAMERArunGCrunLCshowto.msptreat.DBwrite.msp

Dependencies:abindaffyaffyioAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsbiocmakeBiocManagerBiocParallelbslibcachemCAMERAcheckmatecliclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIDelayedArrayDEoptimRdigestdir.expirydoParalleldplyrevaluatefarverfastmapfilelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegraphgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmzIDmzRncdf4nnetopensslotelpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchPTModspurrrQFeaturesR6rappdirsRBGLRColorBrewerRcppreshape2Rhdf5librlangrmarkdownrobustbaserpartrstudioapiS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitevsnwithrxcmsxfunXMLXVectoryaml

runLC
Rendered fromrunLC.Rnwusingutils::Sweave

Last update: 2014-08-01
Started: 2014-03-31

runGC
Rendered fromrunGC.Rnwusingutils::Sweave

Last update: 2014-03-31
Started: 2014-03-31

Readme and manuals

Help Manual

Help pageTopics
Analysis pipeline for MS-based metabolomics datametaMS-package metaMS
Add retention index information to an msp objectaddRI
LC alignmentalignmentLC
Annotate a PeaktableAnnotateFeature AnnotateTable
Conversion of a list of annotation results into a tableannotations2tab makeAnnotation
Create a list of all pseudospectra found in a GC-MS experiment of several samples.constructExpPseudoSpectra
Create an in-house database for GC-MS annotationcreateSTDdbGC generateStdDBGC
Create an in-house database for LC-MS annotationcreateSTDdbLC generateStdDBLC
Mass error surface for Waters Synapt Q-TOF spectrometerserrf
Sample table for the generation of a database of standards (LCMS)exptable
Example settings for 'metaMS'FEMsettings Orbitrap.RP Synapt.NP Synapt.RP TSQXLS.GC
Results of metaMS for a small GC-MS data setGCresults
Get LC annotationgetAnnotationLC
Obtain relative quantitative annotation results for GC-MSgetAnnotationMat relInt
Construct an object containing all meta-information of the annotated pseudospectra (GC-MS).getFeatureInfo
Extract a peak table from an xcms or CAMERA objectgetPeakTable
Sample DB for LC-MS annotationLCDBtest
Result metaMS for a small LC-MS data setLCresults LCxset
Match GC-MS spectra to an external reference DBmatch2ExtDB
Match a GC-MS pseudospectrum to a database with a weighted crossproduct criterion.matchExpSpec
Match pseudospectra from several samples to an in-house DB (GC-MS)matchSamples2DB
Compare pseudospectra across samples (GC-MS)match.unannot.patterns matchSamples2Samples
Class '"metaMSsettings"'metaMSsettings metaMSsettings-class show,metaMSsettings-method
Get or set values in metaMSsettings objectsmetaSetting metaSetting,metaMSsettings-method metaSetting<- metaSetting<-,metaMSsettings-method
Functions to handle msp-type objects (GC-MS)construct.msp filter.msp msp read.msp SearchNIST to.msp write.msp xset2msp
Wrapper for XCMS peak detection, to be used for both GC-MS and LC-MS data.peakDetection
Plot a pseudospectrum.plotPseudoSpectrum
Functions for metaMS-formatted text outputprintInfo printString printWarning
Process input files containing raw data for pure standards.processStandards
Read information of GC injections of standards from a csv filereadStdInfo
Remove double m/z entries in a pseudospectrumremoveDoubleMasses
The CAMERA element in the metaMS pipelinerunCAMERA
Wrapper for processing of GC-MS data filesrunGC
Wrapper for processing of LC-MS data filesrunLC
Information on three chemical standards measured in GC-MS (liquid injection)DB smallDB stdInfo threeStdsDB threeStdsInfo threeStdsNIST
Scaling of pseudospectra in an msp objecttreat.DB