findFeaturesXCMS3: Find features using XCMS (new interface)

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

Find features using XCMS (new interface)

Description

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

Usage

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.

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.

Value

An object of a class which is derived from features.

References

\addCitations

xcms1

\addCitationsxcms2

\addCitationsxcms3

See Also

findFeatures for more details and other algorithms.

rickhelmus/patRoon documentation built on Nov. 22, 2024, 3:11 p.m.