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## This is a MALDIquant example file. It is released into public domain with the
## right to use it for any purpose but without any warranty.
## warping demo
## load necessary packages
## requires MALDIquant >= 1.9
library("MALDIquant")
## load example spectra
data("fiedler2009subset", package="MALDIquant")
## use only 4 spectra
spectra <- fiedler2009subset[seq(1, 16, by=4)]
## some preprocessing
## sqrt transform (for variance stabilization)
spectra <- transformIntensity(spectra, method="sqrt")
## 21 point Savitzky-Golay-Filter for smoothing spectra
spectra <- smoothIntensity(spectra, method="SavitzkyGolay", halfWindowSize=10)
## remove baseline
spectra <- removeBaseline(spectra, method="SNIP", iterations=100)
## calibrate intensity values by "Total Ion Current"
spectra <- calibrateIntensity(spectra, method="TIC")
## run peak detection
peaks <- detectPeaks(spectra, method="MAD", halfWindowSize=20, SNR=2)
## warping
par(mfrow=c(2, 2))
warpingFunctions <- determineWarpingFunctions(peaks, tolerance=0.001,
plot=TRUE, plotInteractive=TRUE)
## warp spectra
warpedSpectra <- warpMassSpectra(spectra, warpingFunctions)
## warp peaks
warpedPeaks <- warpMassPeaks(peaks, warpingFunctions)
## compare some regions in a plot
par(mfrow=c(2, 2))
## helper function to avoid double coding
plotSpectra <- function(unwarped, warped, range) {
plot(unwarped[[1]], main=paste0("unwarped spectra (mass ",
paste0(range, collapse=":"), " Da)"),
xlim=range, ylim=c(0, 2e-3), type="n")
color <- rainbow(length(unwarped))
for (i in seq(along=unwarped)) {
lines(unwarped[[i]], col=color[i])
}
plot(unwarped[[1]], main=paste0("warped spectra (mass ",
paste0(range, collapse=":"), " Da)"),
xlim=range, ylim=c(0, 2e-3), type="n")
for (i in seq(along=warped)) {
lines(warped[[i]], col=color[i])
}
}
plotSpectra(spectra, warpedSpectra, c(4180, 4240))
plotSpectra(spectra, warpedSpectra, c(9200, 9400))
par(mfrow=c(1, 1))
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