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Conversion to XCMS objects

Source: R/generics.R, R/utils-xcms.R
xcms-conv.Rd

Converts a features or featureGroups object to an xcmsSet or XCMSnExp object.

Usage

getXCMSSet(obj, verbose = TRUE, ...)

getXCMSnExp(obj, verbose = TRUE, ...)

# S4 method for class 'features'
getXCMSSet(obj, verbose, loadRawData, IMS = FALSE)

# S4 method for class 'featuresXCMS'
getXCMSSet(obj, verbose = TRUE, ...)

# S4 method for class 'featureGroups'
getXCMSSet(obj, verbose, loadRawData, IMS = FALSE)

# S4 method for class 'featureGroupsXCMS'
getXCMSSet(obj, verbose, loadRawData, ...)

# S4 method for class 'featuresSet'
getXCMSSet(obj, ..., set)

# S4 method for class 'featureGroupsSet'
getXCMSSet(obj, ..., set)

# S4 method for class 'features'
getXCMSnExp(obj, verbose, loadRawData, IMS = FALSE)

# S4 method for class 'featuresXCMS3'
getXCMSnExp(obj, verbose = TRUE, ...)

# S4 method for class 'featureGroups'
getXCMSnExp(obj, verbose, loadRawData, IMS = FALSE)

# S4 method for class 'featureGroupsXCMS3'
getXCMSnExp(obj, verbose, loadRawData, ...)

# S4 method for class 'featuresSet'
getXCMSnExp(obj, ..., set)

# S4 method for class 'featureGroupsSet'
getXCMSnExp(obj, ..., set)

Arguments

obj

The object that should be converted.

verbose

If FALSE then no text output is shown.

...

(sets workflow) Further arguments passed to non-sets method.

Otherwise ignored.

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.

IMS

(IMS workflow) Specifies which feature groups are considered for export in IMS workflows. The following options are valid:

  • "both": Selects IMS and non-IMS features.

  • "maybe": Selects non-IMS features and IMS features without assigned IMS precursor.

  • FALSE: Selects only non-IMS features.

  • TRUE: Selects only IMS features.

This should be kept FALSE as XCMS export currently does not support IMS features.

set

(sets workflow) The name of the set to be exported.

Details

The conversion process will introduce some dummy values for metadata not present in patRoon objects. If the features or featureGroups object was generated with XCMS, then no conversion is performed and the original XCMS object will be returned, if possible. Conversion may still occur e.g. due to the application of some subsetting or filtering steps or the re-ordering of analyses.

Sets workflows

In a sets workflow, unset is used to convert the feature (group) data before the object is exported.

References

reference 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.