metaMS: MS-based metabolomics annotation pipeline
Version 1.12.0

MS-based metabolomics data processing and compound annotation pipeline.

Browse man pages Browse package API and functions Browse package files

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)
Bioconductor views MassSpectrometry Metabolomics
Date of publicationNone
MaintainerRon Wehrens <ron.wehrens@gmail.com>
LicenseGPL (>= 2)
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("metaMS")

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

Functions

AnnotateFeature Man page Source code
AnnotateTable Man page Source code
DB Man page
FEMsettings Man page
GCresults Man page
LCDBtest Man page
LCresults Man page
LCxset Man page
Synapt.NP Man page
Synapt.RP Man page
TSQXLS.GC Man page
addRI Man page Source code
alignmentLC Man page Source code
annotations2tab Man page Source code
construct.msp Man page Source code
constructExpPseudoSpectra Man page Source code
createSTDdbGC Man page Source code
createSTDdbLC Man page Source code
errf Man page
exptable Man page
filter.msp Man page Source code
generateStdDBGC Man page Source code
generateStdDBLC Man page Source code
getAnnotationLC Man page Source code
getAnnotationMat Man page Source code
getFeatureInfo Man page Source code
getPeakTable Man page Source code
makeAnnotation Man page Source code
match.unannot.patterns Man page Source code
match2ExtDB Man page Source code
matchExpSpec Man page Source code
matchSamples2DB Man page Source code
matchSamples2Samples Man page Source code
metaMS Man page
metaMS-package Man page
metaMSsettings Man page
metaMSsettings-class Man page
metaSetting Man page
metaSetting,metaMSsettings Man page
metaSetting,metaMSsettings-method Man page
metaSetting-methods Man page
metaSetting<- Man page
metaSetting<-,metaMSsettings Man page
metaSetting<-,metaMSsettings-method Man page
msp Man page
mzmatch Man page Source code
peakDetection Man page Source code
plotPseudoSpectrum Man page Source code
printInfo Man page Source code
printString Man page Source code
printWarning Man page Source code
processStandards Man page Source code
read.msp Man page Source code
readStdInfo Man page Source code
relInt Man page Source code
removeDoubleMasses Man page Source code
runCAMERA Man page Source code
runGC Man page Source code
runLC Man page Source code
show,metaMSsettings-method Man page
smallDB Man page
stdInfo Man page
threeStdsDB Man page
threeStdsInfo Man page
threeStdsNIST Man page
to.msp Man page Source code
treat.DB Man page Source code
write.msp Man page Source code
xset2msp Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/addRI.R
R/alignmentLC.R
R/annotate.R
R/annotations2tab.R
R/constructExpPseudoSpectra.R
R/createSTDdbGC.R
R/createSTDdbLC.R
R/generateStdDBGC.R
R/generateStdDBLC.R
R/getAnnotationLC.R
R/getAnnotationMat.R
R/getFeatureInfo.R
R/getPeakTable.R
R/matchSamples2DB.R
R/matchSamples2Samples.R
R/matchfuns.R
R/metaMSsettings.R
R/msp.R
R/peakDetection.R
R/plotPseudoSpectrum.R
R/printString.R
R/processStandards.R
R/readStdInfo.R
R/relInt.R
R/runCAMERA.R
R/runGC.R
R/runLC.R
README.md
build
build/vignette.rds
data
data/FEMsettings.RData
data/GCresults.RData
data/LCDBtest.RData
data/LCresults.RData
data/datalist
data/errf.RData
data/exptable.RData
data/threeStdsDB.RData
data/threeStdsInfo.RData
data/threeStdsNIST.RData
inst
inst/CITATION
inst/doc
inst/doc/runGC.R
inst/doc/runGC.Rnw
inst/doc/runGC.pdf
inst/doc/runLC.R
inst/doc/runLC.Rnw
inst/doc/runLC.pdf
inst/scripts
inst/scripts/GCdata.R
inst/scripts/LCdata.R
inst/unitTests
inst/unitTests/test_GC.R
inst/unitTests/test_LC.R
man
man/AnnotateTable.Rd
man/FEMsettings.Rd
man/GCresults.Rd
man/LCDBtest.Rd
man/LCresults.Rd
man/addRI.Rd
man/alignmentLC.Rd
man/annotations2tab.Rd
man/constructExpPseudoSpectra.Rd
man/createSTDdbGC.Rd
man/createSTDdbLC.Rd
man/errf.Rd
man/exptable.Rd
man/getAnnotationLC.Rd
man/getAnnotationMat.Rd
man/getFeatureInfo.Rd
man/getPeakTable.Rd
man/match2ExtDB.Rd
man/matchExpSpec.Rd
man/matchSamples2DB.Rd
man/matchSamples2Samples.Rd
man/metaMS-package.Rd
man/metaMSsettings-class.Rd
man/metaSetting-methods.Rd
man/msp.Rd
man/peakDetection.Rd
man/plotPseudoSpectrum.Rd
man/printString.Rd
man/processStandards.Rd
man/readStdInfo.Rd
man/removeDoubleMasses.Rd
man/runCAMERA.Rd
man/runGC.Rd
man/runLC.Rd
man/threeStdsDB.Rd
man/treat.DB.Rd
tests
tests/runTests.R
vignettes
vignettes/GC.bib
vignettes/LC.bib
vignettes/runGC.Rnw
vignettes/runLC.Rnw
metaMS documentation built on May 20, 2017, 9:55 p.m.