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

Functions

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

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.