metaMS: MS-based metabolomics annotation pipeline

MS-based metabolomics data processing and compound annotation pipeline.

Author
Ron 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 publication
None
Maintainer
Ron Wehrens <ron.wehrens@gmail.com>
License
GPL (>= 2)
Version
1.10.0

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