MALDIquant (version 1.18)

warpMassSpectra: 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.

Value

Returns a list of warped '>MassPeaks or '>MassSpectrum objects.

Details

The warping function w is called in the following way: $$newMass = oldMass + w(oldMass)$$

See Also

determineWarpingFunctions, '>MassPeaks, '>MassSpectrum

Website: http://strimmerlab.org/software/maldiquant/

Examples

# NOT RUN {
## 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)
# }