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.
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
runLC - in-house databases are created by functions
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 <email@example.com>
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