warp-functions: Run warping functions on AbstractMassObject objects.

In MALDIquant: Quantitative Analysis of Mass Spectrometry Data

Run warping functions on AbstractMassObject objects.

Description

These functions run warping functions on AbstractMassObject objects (warping is also known as phase correction).

Usage

warpMassPeaks(l, w, emptyNoMatches=FALSE)

warpMassSpectra(l, w, emptyNoMatches=FALSE)

Arguments

l	list, list of MassPeaks or MassSpectrum objects.
w	a list of warping functions determined by determineWarpingFunctions. Has to be of the same length as l.
emptyNoMatches	logical, if TRUE (default: FALSE) the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero.

Details

The warping function w is called in the following way:

newMass = oldMass + w(oldMass)

Value

Returns a list of warped MassPeaks or MassSpectrum objects.

Author(s)

Sebastian Gibb [e-mail]

See Also

determineWarpingFunctions, MassPeaks, MassSpectrum

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

Examples

## load package
library("MALDIquant")

## create a MassPeaks object
p <- createMassPeaks(mass=1:5, intensity=1:5)

## stupid warping function for demonstration
## (please use determineWarpingFunctions in real life applications)
simpleWarp <- function(x) { return(1) }

## run warping function
w <- warpMassPeaks(list(p), list(simpleWarp))[[1]]

## compare results
all(mass(w) == mass(p)+1) # TRUE

## no warping (MassPeaks object is not changed)
warpMassPeaks(list(p), list(NA))

## no warping (intensity values of MassPeaks object are set to zero)
warpMassPeaks(list(p), list(NA), emptyNoMatches=TRUE)

MALDIquant documentation built on March 31, 2023, 10:40 p.m.