Find features using XCMS (new interface)

Uses the new xcms3 interface from the xcms package to find features.

findFeaturesXCMS3(
  analysisInfo,
  param = xcms::CentWaveParam(),
  ...,
  verbose = TRUE
)

Arguments

analysisInfo

A data.frame with Analysis information.

param

The method parameters used by XCMS peak finding, see xcms::findChromPeaks

...

Further parameters passed to xcms::findChromPeaks.

verbose

If set to FALSE then no text output is shown.

Value

An object of a class which is derived from features.

Details

This function uses XCMS3 to automatically find features. This function is called when calling findFeatures with algorithm="xcms3".

The file format of analyses must be mzML or mzXML.

The input MS data files need to be centroided. The convertMSFiles function can be used to centroid data.

References

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

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.

See also

findFeatures for more details and other algorithms.