findFeaturesXCMS: Find features using XCMS (old interface)

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

Find features using XCMS (old interface)

Description

Uses the legacy xcmsSet function from the xcms package to find features.

Usage

findFeaturesXCMS(analysisInfo, method = "centWave", ..., verbose = TRUE)

Arguments

analysisInfo	A data.frame with Analysis information.
method	The method setting used by XCMS peak finding, see xcms::findPeaks
...	Further parameters passed to xcmsSet.
verbose	If set to FALSE then no text output is shown.

Details

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

This function uses the legacy interface of xcms. It is recommended to use findFeaturesXCMS3 instead.

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.

findFeaturesXCMS3

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