MALDIquant (version 1.22.3)

alignSpectra: 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, ...)

Value

Returns a list of aligned MassSpectrum objects.

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.

Author

Sebastian Gibb

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).

See Also

detectPeaks, determineWarpingFunctions, referencePeaks, warpMassSpectra, MassSpectrum

demo("warping")

Website: https://strimmerlab.github.io/software/maldiquant/

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)