# MS-based metabolomics annotation pipeline

## Documentation for package ‘metaMS’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

metaMS-package | Analysis pipeline for MS-based metabolomics data
addRI | Add retention index information to an msp object
alignmentLC | LC alignment
AnnotateFeature | Annotate a Peaktable
AnnotateTable | Annotate a Peaktable
annotations2tab | Conversion of a list of annotation results into a table
construct.msp | Functions to handle msp-type objects (GC-MS)
constructExpPseudoSpectra | Create a list of all pseudospectra found in a GC-MS experiment of several samples.
createSTDdbGC | Create an in-house database for GC-MS annotation
createSTDdbLC | Create an in-house database for LC-MS annotation
DB | Information on three chemical standards measured in GC-MS (liquid injection)
errf | Mass error surface for Waters Synapt Q-TOF spectrometers
exptable | Sample table for the generation of a database of standards (LCMS)
FEMsettings | Example settings for 'metaMS'
filter.msp | Functions to handle msp-type objects (GC-MS)
GCresults | Results of metaMS for a small GC-MS data set
generateStdDBGC | Create an in-house database for GC-MS annotation
generateStdDBLC | Create an in-house database for LC-MS annotation
getAnnotationLC | Get LC annotation
getAnnotationMat | Obtain relative quantitative annotation results for GC-MS
getFeatureInfo | Construct an object containing all meta-information of the annotated pseudospectra (GC-MS).
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
LCxset | Result metaMS for a small LC-MS data set
makeAnnotation | Conversion of a list of annotation results into a table
match.unannot.patterns | Compare pseudospectra across samples (GC-MS)
match2ExtDB | Match GC-MS spectra to an external reference DB
matchExpSpec | Match a GC-MS pseudospectrum to a database with a weighted crossproduct criterion.
matchSamples2DB | Match pseudospectra from several samples to an in-house DB (GC-MS)
matchSamples2Samples | Compare pseudospectra across samples (GC-MS)
metaMS | Analysis pipeline for MS-based metabolomics data
metaMSsettings | Class '"metaMSsettings"'
metaMSsettings-class | Class '"metaMSsettings"'
metaSetting | Get or set values in metaMSsettings objects
metaSetting-method | Get or set values in metaMSsettings objects
metaSetting<- | Get or set values in metaMSsettings objects
metaSetting<--method | Get or set values in metaMSsettings objects
msp | Functions to handle msp-type objects (GC-MS)
Orbitrap.RP | Example settings for 'metaMS'
peakDetection | Wrapper for XCMS peak detection, to be used for both GC-MS and LC-MS data.
plotPseudoSpectrum | Plot a pseudospectrum.
printInfo | Functions for metaMS-formatted text output
printString | Functions for metaMS-formatted text output
printWarning | Functions for metaMS-formatted text output
processStandards | Process input files containing raw data for pure standards.
read.msp | Functions to handle msp-type objects (GC-MS)
readStdInfo | Read information of GC injections of standards from a csv file
relInt | Obtain relative quantitative annotation results for GC-MS
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
SearchNIST | Functions to handle msp-type objects (GC-MS)
show-method | Class '"metaMSsettings"'
smallDB | Information on three chemical standards measured in GC-MS (liquid injection)
stdInfo | Information on three chemical standards measured in GC-MS (liquid injection)
Synapt.NP | Example settings for 'metaMS'
Synapt.RP | Example settings for 'metaMS'
threeStdsDB | Information on three chemical standards measured in GC-MS (liquid injection)
threeStdsInfo | Information on three chemical standards measured in GC-MS (liquid injection)
threeStdsNIST | Information on three chemical standards measured in GC-MS (liquid injection)
to.msp | Functions to handle msp-type objects (GC-MS)
treat.DB | Scaling of pseudospectra in an msp object
TSQXLS.GC | Example settings for 'metaMS'
write.msp | Functions to handle msp-type objects (GC-MS)
xset2msp | Functions to handle msp-type objects (GC-MS)