metaMS: MS-based metabolomics annotation pipeline

MS-based metabolomics data processing and compound annotation pipeline.

AuthorRon Wehrens [aut, cre] (author of GC-MS part), Pietro Franceschi [aut] (author of LC-MS part), Nir Shahaf [ctb], Matthias Scholz [ctb], Georg Weingart [ctb] (development of GC-MS approach), Elisabete Carvalho [ctb] (testing and feedback of GC-MS pipeline)
Date of publicationNone
MaintainerRon Wehrens <ron.wehrens@gmail.com>
LicenseGPL (>= 2)
Version1.10.0

View on Bioconductor

Man pages

addRI: Add retention index information to an msp object

alignmentLC: LC alignment

AnnotateTable: Annotate a Peaktable

annotations2tab: Conversion of a list of annotation results into a table

constructExpPseudoSpectra: Create a list of all pseudospectra found in a GC-MS...

createSTDdbGC: Create an in-house database for GC-MS annotation

createSTDdbLC: Create an in-house database for LC-MS annotation

errf: Mass error surface for Waters Synapt Q-TOF spectrometers

exptable: Sample table for the generation of a database of standards...

FEMsettings: Example settings for 'metaMS'

GCresults: Results of metaMS for a small GC-MS data set

getAnnotationLC: Get LC annotation

getAnnotationMat: Obtain relative quantitative annotation results for GC-MS

getFeatureInfo: Construct an object containing all meta-information of the...

getPeakTable: Extract a peak table from an xcms or CAMERA object

LCDBtest: Sample DB for LC-MS annotation

LCresults: Result metaMS for a small LC-MS data set

match2ExtDB: Match GC-MS spectra to an external reference DB

matchExpSpec: Match a GC-MS pseudospectrum to a database with a weighted...

matchSamples2DB: Match pseudospectra from several samples to an in-house DB...

matchSamples2Samples: Compare pseudospectra across samples (GC-MS)

metaMS-package: Analysis pipeline for MS-based metabolomics data

metaMSsettings-class: Class '"metaMSsettings"'

metaSetting-methods: Get or set values in metaMSsettings objects

msp: Functions to handle msp-type objects (GC-MS)

peakDetection: Wrapper for XCMS peak detection, to be used for both GC-MS...

plotPseudoSpectrum: Plot a pseudospectrum.

printString: Functions for metaMS-formatted text output

processStandards: Process input files containing raw data for pure standards.

readStdInfo: Read information of GC injections of standards from a csv...

removeDoubleMasses: Remove double m/z entries in a pseudospectrum

runCAMERA: The CAMERA element in the metaMS pipeline

runGC: Wrapper for processing of GC-MS data files

runLC: Wrapper for processing of LC-MS data files

threeStdsDB: Information on three chemical standards measured in GC-MS...

treat.DB: Scaling of pseudospectra in an msp object

Files in this package

metaMS/DESCRIPTION
metaMS/NAMESPACE
metaMS/NEWS
metaMS/R
metaMS/R/addRI.R metaMS/R/alignmentLC.R metaMS/R/annotate.R metaMS/R/annotations2tab.R metaMS/R/constructExpPseudoSpectra.R metaMS/R/createSTDdbGC.R metaMS/R/createSTDdbLC.R metaMS/R/generateStdDBGC.R metaMS/R/generateStdDBLC.R metaMS/R/getAnnotationLC.R metaMS/R/getAnnotationMat.R metaMS/R/getFeatureInfo.R metaMS/R/getPeakTable.R metaMS/R/matchSamples2DB.R metaMS/R/matchSamples2Samples.R metaMS/R/matchfuns.R metaMS/R/metaMSsettings.R metaMS/R/msp.R metaMS/R/peakDetection.R metaMS/R/plotPseudoSpectrum.R metaMS/R/printString.R metaMS/R/processStandards.R metaMS/R/readStdInfo.R metaMS/R/relInt.R metaMS/R/runCAMERA.R metaMS/R/runGC.R metaMS/R/runLC.R
metaMS/README.md
metaMS/build
metaMS/build/vignette.rds
metaMS/data
metaMS/data/FEMsettings.RData
metaMS/data/GCresults.RData
metaMS/data/LCDBtest.RData
metaMS/data/LCresults.RData
metaMS/data/datalist
metaMS/data/errf.RData
metaMS/data/exptable.RData
metaMS/data/threeStdsDB.RData
metaMS/data/threeStdsInfo.RData
metaMS/data/threeStdsNIST.RData
metaMS/inst
metaMS/inst/CITATION
metaMS/inst/doc
metaMS/inst/doc/runGC.R
metaMS/inst/doc/runGC.Rnw
metaMS/inst/doc/runGC.pdf
metaMS/inst/doc/runLC.R
metaMS/inst/doc/runLC.Rnw
metaMS/inst/doc/runLC.pdf
metaMS/inst/scripts
metaMS/inst/scripts/GCdata.R
metaMS/inst/scripts/LCdata.R
metaMS/inst/unitTests
metaMS/inst/unitTests/test_GC.R
metaMS/inst/unitTests/test_LC.R
metaMS/man
metaMS/man/AnnotateTable.Rd metaMS/man/FEMsettings.Rd metaMS/man/GCresults.Rd metaMS/man/LCDBtest.Rd metaMS/man/LCresults.Rd metaMS/man/addRI.Rd metaMS/man/alignmentLC.Rd metaMS/man/annotations2tab.Rd metaMS/man/constructExpPseudoSpectra.Rd metaMS/man/createSTDdbGC.Rd metaMS/man/createSTDdbLC.Rd metaMS/man/errf.Rd metaMS/man/exptable.Rd metaMS/man/getAnnotationLC.Rd metaMS/man/getAnnotationMat.Rd metaMS/man/getFeatureInfo.Rd metaMS/man/getPeakTable.Rd metaMS/man/match2ExtDB.Rd metaMS/man/matchExpSpec.Rd metaMS/man/matchSamples2DB.Rd metaMS/man/matchSamples2Samples.Rd metaMS/man/metaMS-package.Rd metaMS/man/metaMSsettings-class.Rd metaMS/man/metaSetting-methods.Rd metaMS/man/msp.Rd metaMS/man/peakDetection.Rd metaMS/man/plotPseudoSpectrum.Rd metaMS/man/printString.Rd metaMS/man/processStandards.Rd metaMS/man/readStdInfo.Rd metaMS/man/removeDoubleMasses.Rd metaMS/man/runCAMERA.Rd metaMS/man/runGC.Rd metaMS/man/runLC.Rd metaMS/man/threeStdsDB.Rd metaMS/man/treat.DB.Rd
metaMS/tests
metaMS/tests/runTests.R
metaMS/vignettes
metaMS/vignettes/GC.bib
metaMS/vignettes/LC.bib
metaMS/vignettes/runGC.Rnw
metaMS/vignettes/runLC.Rnw

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