runGC: Wrapper for processing of GC-MS data files

In rwehrens/metaMS: MS-based metabolomics annotation pipeline

Wrapper for processing of GC-MS data files

Description

Main function of the pipeline for GC-MS data processing. It includes XCMS peak detection, definition of pseudospectra, and compound identification by comparison to a database of standards. The function also takes care of removal of artefacts like column bleeding and plasticizers, and definition of unknowns, consistently present across samples.

Usage

runGC(files, xset, settings, rtrange = NULL, DB = NULL,
      removeArtefacts = TRUE, findUnknowns = nexp >= mcs,
      returnXset = FALSE, RIstandards = NULL, nSlaves = 0)
      

Arguments

files	input files, given as a vector of strings containing the complete paths. All formats supported by XCMS can be used.
xset	alternatively, one can present a list of xcmsSet objects for whom CAMERA grouping has been done. In this case, only the annotation process will be done. If both files and xset are given, the former takes precedence.
settings	a nested list of settings, to be used at individual steps of the pipeline.
rtrange	part of the chromatograms that is to be analysed. If given, it should be a vector of two numbers indicating minimal and maximal retention time (in minutes).
DB	database containing the spectra of the pure standards. At least the following fields should be present: Name, std.rt, pspectrum and monoMW.
removeArtefacts	logical, whether or not to remove patterns identified as (e.g.) column bleeding. Only performed if a database containing such patterns is available.
findUnknowns	logical, whether to find patterns without identification that are present consistently in several samples. The default is to use TRUE if the number of samples is larger than the min.class.size setting in the 'betweenSamples' metaSetting.
returnXset	logical: should the XCMS output be returned? If yes, this is a a list of xcmsSet objects, one element for each input file.
RIstandards	A two-column matrix containing for the standards defining the RI scale both retention times and retention indices. If not given, no RI values will be calculated and retention times will be used instead.
nSlaves	Number of cores to be used in peak picking.

Value

A list with the following elements:

PeakTable	data.frame containing annotation information. Every line is a feature, i.e. a pseudospectrum. The first columns are used to give information about these features, a.o. compound name, CAS and Chemspider IDs, etcetera. The last of these meta-information columns is always the one giving the retention time: “rt”. After that, columns correspond to input files, and give measures of intensities for every single one of the features. If a feature is not detected in a sample, this is indicated with “0” (zero).
PseudoSpecra	A list of pseudospectra in msp format, in the same order as the rows in the PeakTable.
xset	optionally, the xcmsSet object is returned, which can be useful for more detailed inspection of the results. It can also be used as an input for runGC, e.g., to test different annotation settings independently of the xcms/CAMERA part.
sessionInfo	The output of sessionInfo() to keep track of the sw version used for the processing

Author(s)

Ron Wehrens

References

R. Wehrens, G. Weingart and F. Mattivi: "An open-source pipeline for GC-MS-based untargeted metabolomics". Submitted.

See Also

msp, treat.DB, runCAMERA, peakDetection, matchSamples2DB, matchSamples2Samples, getAnnotationMat, addRI

Examples

## analysis of an xset object
data(threeStdsDB) 
data(FEMsettings)

data(GCresults) ## pre-compiled results
names(GCresults)

## Not run: 
if (require(metaMSdata)) {
  ## object GCresults is created by
  cdfdir <- system.file("extdata", package = "metaMSdata")
  cdffiles <- list.files(cdfdir, pattern = "_GC_",
                         full.names = TRUE, ignore.case = TRUE)
  GCresults <- runGC(files = cdffiles, settings = TSQXLS.GC, DB = DB,
                     returnXset = TRUE)

  ## to start directly from the XCMS/CAMERA results and not include
  ## peak picking in the pipeline, simply provide the "xset" argument
  ## rather than the "files" argument.

  ## no annotation database
  result.noannot <- runGC(xset = GCresults$xset, settings = TSQXLS.GC)
  }

## End(Not run)

rwehrens/metaMS documentation built on Feb. 27, 2023, 5:13 a.m.