processProteinSpectra: Process protein spectra with MALDIquant

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

Process protein spectra with MALDIquant

Description

Process protein spectra with MALDIquant

Usage

processProteinSpectra(
  input,
  smoothIntensityMethod = "SavitzkyGolay",
  removeBaselineMethod = "TopHat",
  detectPeaksMethod = "MAD",
  transformIntensityMethod = "sqrt",
  halfWindowSize = 20L,
  minSNR = 3
)

Arguments

input	MALDIquant mass spectrum list
smoothIntensityMethod	see ?MALDIquant::smoothIntensity
removeBaselineMethod	see ?MALDIquant::smoothIntensity
detectPeaksMethod	see ?MALDIquant::detectPeaks
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.
minSNR	see ?MALDIquant::detectPeaks

Value

MALDIquant mass spectrum list

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