Group features using XCMS (old interface)

Group and align features with the legacy xcmsSet function from the xcms package.

Usage

groupFeaturesXCMS(feat, ...)

# S4 method for class 'features'
groupFeaturesXCMS(
  feat,
  rtalign = TRUE,
  loadRawData = TRUE,
  groupArgs = list(mzwid = 0.015),
  retcorArgs = list(method = "obiwarp"),
  verbose = TRUE
)

# S4 method for class 'featuresSet'
groupFeaturesXCMS(feat, groupArgs = list(mzwid = 0.015), verbose = TRUE)

Arguments

feat: The features object with the features to be grouped.
...: Further parameters passed to the selected grouping algorithm.
rtalign: Set to TRUE to enable retention time alignment.
loadRawData: Set to TRUE if analyses are available as mzXML or mzML files. Otherwise MS data is not loaded, and some dummy data (e.g. file paths) is used in the returned object.
groupArgs: named character vector that may contain extra grouping parameters to be used by xcms::group
retcorArgs: named character vector that may contain extra parameters to be used by xcms::retcor.
verbose: if FALSE then no text output will be shown.

Value

An object of a class which is derived from featureGroups.

Details

This function uses XCMS to group features. This function is called when calling groupFeatures with algorithm="xcms".

Grouping of features and alignment of their retention times are performed with the xcms::group and xcms::retcor functions, respectively. Both functions have an extensive list of parameters to modify their behavior and may therefore be used to potentially optimize results.

Sets workflows

loadRawData and arguments related to retention time alignment are currently not supported for sets workflows.

References

Benton HP, Want EJ, Ebbels TMD (2010). “Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data.” BIOINFORMATICS, 26, 2488.

Louail P, Brunius C, Garcia-Aloy M, Kumler W, Storz N, Stanstrup J, Treutler H, Vangeenderhuysen P, Witting M, Neumann S, Rainer J (2025). “xcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem.” Analytical Chemistry. doi:10.1021/acs.analchem.5c04338 . https://doi.org/10.1021/acs.analchem.5c04338.

Smith, C.A., Want, E.J., O'Maille, G., Abagyan,R., Siuzdak, G. (2006). “XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification.” Analytical Chemistry, 78, 779–787.

Tautenhahn R, Boettcher C, Neumann S (2008). “Highly sensitive feature detection for high resolution LC/MS.” BMC Bioinformatics, 9, 504.