preprocessMS {MGMS2}

preprocessMS

Description

Internal function. This function preprocesses spectra by transforming/smoothing intensity, removing baseline, and calibrating intensities.

Usage

preprocessMS(spectra, halfWindowSize = 20, SNIP.iteration = 60)

Arguments

spectra

Spectra. A MALDIquant object. An output of either importMzXml or filtermass.

halfWindowSize

halfWindowSize The highest peaks in the given window (+/-halfWindowSize) will be recognized as peaks. (Default: 20). See detectPeaks for details.

SNIP.iteration

SNIP.iteration An iteration used to remove the baseline of an spectrum. (Default: 60). See removeBaseline for details.

Value

The processed mass spectra. A list of MALDIquant MassSpectrum objects (S4 objects).