metaMS-package {metaMS} | R Documentation

## Analysis pipeline for MS-based metabolomics data

### Description

Analysis pipeline for MS-based metabolomics data: basic peak picking and grouping is done using functions from packages xcms and CAMERA. The main output is a table of feature intensities in all samples, which can immediately be analysed with multivariate methdos. The package supports the creation of in-house databases of mass spectra (including retention information) of pure chemical compounds. Such databases can then be used for annotation purposes.

### Details

Index:

    AnnotateFeature         Feature Wise Annotation
    AnnotateTable           AnnotateTable
    FEMsettings             FEM Settings for 'metaMS'
    LCDBtest                Sample DB for LC-MS annotation
    alignmentLC             LC alignment
    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
    exptable                Sample table for DB generation (LC)
    generateStdDBGC         Convert an msp object into a GC database object
    getAnnotationLC         get LC annotation
    getAnnotationMat        Subfunction GC-MS processing
    getFeatureInfo          Construct an object containing all
                            meta-information of the annotated pseudospectra
                            (GC-MS).
    getPeakTable            get peak table
    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)
    peakDetection           Wrapper for XCMS peak detection, to be used for
                            both GC-MS and LC-MS data.
    plotPseudoSpectrum      Plot a pseudospectrum.
    processStandards        Process input files containing raw data for
                            pure standards.
    readStdInfo             Read information of injections of standards
                            from a csv file.
    runCAMERA               Run CAMERA
    runGC                   Wrapper for processing of GC-MS data files
    runLC                   Wrapper for processing of LC-MS data files
    treat.DB                Scaling of pseudospectra in an msp object.

The most important functions for running the pipeline are `runGC` and `runLC` - in-house databases are created by functions `createSTDdbGC` and `createSTDdbLC`.

### Author(s)

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)

Maintainer: Ron Wehrens <ron.wehrens@fmach.it>

[Package metaMS version 1.22.0 Index]