normalizeSpectrumIntensity: Smooth, remove baseline, and normalize intensity of a...

In chasemc/IDBacApp: MALDI-TOF MS Protien and Small Molecule Analysis

Smooth, remove baseline, and normalize intensity of a spectrum

Description

Smooth, remove baseline, and normalize intensity of a spectrum

Usage

normalizeSpectrumIntensity(
  spectrum,
  smoothIntensityMethod = "SavitzkyGolay",
  removeBaselineMethod = "TopHat",
  calibrateIntensityMethod = "median",
  transformIntensityMethod = "sqrt",
  halfWindowSize = 20L
)

Arguments

spectrum	MALDIquant spectrum
smoothIntensityMethod	see ?MALDIquant::smoothIntensity
removeBaselineMethod	see ?MALDIquant::smoothIntensity
calibrateIntensityMethod	see ?MALDIquant::calibrateIntensityMethod
transformIntensityMethod	see ?MALDIquant::transformIntensity
halfWindowSize	half window size. The resulting window reaches from mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize] (window size is 2*halfWindowSize+1). The best size differs depending on the selected method.

Value

MALDIquant mass spectrum

chasemc/IDBacApp documentation built on Oct. 22, 2022, 2:52 a.m.