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metaMS

data processing for MS-based metabolomics

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Version

Version

1.8.0

License

GPL (>= 2)

Maintainer

Ron Wehrens

Last Published

February 15th, 2017

Functions in metaMS (1.8.0)

LCDBtest

Sample DB for LC-MS annotation
getAnnotationLC

Get LC annotation
errf

Mass error surface for Waters Synapt Q-TOF spectrometers
processStandards

Process input files containing raw data for pure standards.
GCresults

Results of metaMS for a small GC-MS data set
getAnnotationMat

Obtain relative quantitative annotation results for GC-MS
threeStdsDB

Information on three chemical standards measured in GC-MS (liquid injection)
annotations2tab

Conversion of a list of annotation results into a table
metaMSsettings-class

Class "metaMSsettings"
constructExpPseudoSpectra

Create a list of all pseudospectra found in a GC-MS experiment of several samples.
exptable

Sample table for the generation of a database of standards (LCMS)
matchExpSpec

Match a GC-MS pseudospectrum to a database with a weighted crossproduct criterion.
runGC

Wrapper for processing of GC-MS data files
LCresults

Result metaMS for a small LC-MS data set
matchSamples2DB

Match pseudospectra from several samples to an in-house DB (GC-MS)
metaMS-package

Analysis pipeline for MS-based metabolomics data
msp

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

Plot a pseudospectrum.
peakDetection

Wrapper for XCMS peak detection, to be used for both GC-MS and LC-MS data.
treat.DB

Scaling of pseudospectra in an msp object
runLC

Wrapper for processing of LC-MS data files
matchSamples2Samples

Compare pseudospectra across samples (GC-MS)
createSTDdbLC

Create an in-house database for LC-MS annotation
getFeatureInfo

Construct an object containing all meta-information of the annotated pseudospectra (GC-MS).
printString

Functions for metaMS-formatted text output
metaSetting-methods

Get or set values in metaMSsettings objects
addRI

Add retention index information to an msp object
getPeakTable

Extract a peak table from an xcms or CAMERA object
runCAMERA

The CAMERA element in the metaMS pipeline
createSTDdbGC

Create an in-house database for GC-MS annotation
AnnotateTable

Annotate a Peaktable
alignmentLC

LC alignment
FEMsettings

Example settings for metaMS
match2ExtDB

Match GC-MS spectra to an external reference DB
readStdInfo

Read information of GC injections of standards from a csv file
removeDoubleMasses

Remove double m/z entries in a pseudospectrum