alignSpectra-functions: Align MassSpectrum objects.
In MALDIquant: Quantitative Analysis of Mass Spectrometry Data

alignSpectra

R Documentation

Align MassSpectrum objects.

Description

This function aligns a list of MassSpectrum objects (spectra alignment is also known as warping/phase correction).

Usage

alignSpectra(spectra, halfWindowSize=20, noiseMethod="MAD", SNR=2,
  reference, tolerance=0.002, warpingMethod="lowess",
  allowNoMatches=FALSE, emptyNoMatches=FALSE, ...)

Arguments

`spectra`	`list`, list of `MassSpectrum` objects.
`halfWindowSize`	`numeric`, half window size; see `detectPeaks`.
`noiseMethod`	a noise estimation method; see `detectPeaks`.
`SNR`	single numeric value. `SNR` is an abbreviation for signal-to-noise-ratio; see `detectPeaks`.
`reference`	`MassPeaks`, reference object to which the samples (`l`) should be aligned. If missing `referencePeaks` is used; see `determineWarpingFunctions`.
`tolerance`	`double`, maximal relative deviation of a peak position (mass) to be considered as identical. Must be multiplied by `10^-6` for ppm, e.g. use `tolerance=5e-6` for 5 ppm; see `determineWarpingFunctions`.
`warpingMethod`	used basic warping function; see `determineWarpingFunctions`.
`allowNoMatches`	`logical`, don't throw an error if an `MassPeaks` object could not match to the `reference`; see `determineWarpingFunctions`.
`emptyNoMatches`	`logical`, if `TRUE` (default: `FALSE`) the intensity values of `MassSpectrum` or `MassPeaks` objects with missing (`NA`) warping functions are set to zero; see `warpMassSpectra`.
`...`	arguments to be passed to `detectPeaks,MassSpectrum-method`.

Details

alignSpectra is a wrapper function around detectPeaks, determineWarpingFunctions and warpMassSpectra. Please call these functions manually if you need finer control (e.g. plotting of warping functions).

Value

Returns a list of aligned MassSpectrum objects.

Author(s)

Sebastian Gibb mail@sebastiangibb.de

Examples

## load package
library("MALDIquant")

## load example data
data("fiedler2009subset", package="MALDIquant")

## running typical workflow

## transform intensities
spectra <- transformIntensity(fiedler2009subset, method="sqrt")

## smooth spectra
spectra <- smoothIntensity(spectra, method="MovingAverage")

## baseline correction
spectra <- removeBaseline(spectra)

## align spectra
spectra <- alignSpectra(spectra)

MALDIquant documentation built on Sept. 11, 2024, 6:15 p.m.