MALDIquant (version 0.5)

MALDIquant-package: Quantitative analysis of MALDI-TOF MS data

Description

This package is intended to provide an easy-to-use framework for quantitative analysis of MALDI-TOF mass spectrometry data.

MALDIquant is currently under active development. Features available in future versions include peak alignment, quantitative calibration and classification so that MALDIquant is useful for clinical diagnostics.

Details

ll{ Package: MALDIquant Version: 0.5 Date: 2012-01-18 License: GPL (>= 3) URL: http://strimmerlab.org/software/maldiquant/ }

Main classes:

MassPeaks: Represents a peak list of a single spectrum. MassSpectrum: Represents a single spectrum.

References

See website: http://strimmerlab.org/software/maldiquant/

See Also

MassPeaks, MassSpectrum

Examples

## load library
library("MALDIquant");

## load example data
data("sA1", package="MALDIquant");

## show some information
sA1

## running typical workflow

## transform intensities
t <- lapply(sA1, transformIntensity, fun=sqrt);

## smoothing function
movingAvg <- function(y) {
    ma <- rep(1, 5)/5;
    return(filter(y, ma, sides=2));
}

## smooth spectra
s <- lapply(t, transformIntensity, fun=movingAvg);

## baseline correction
b <- lapply(s, removeBaseline);

## detect peaks
p <- lapply(b, detectPeaks);

## plot results
par(mfcol=c(3, length(sA1)));
for (i in seq(along=sA1)) {
    plot(sA1[[i]], main="raw spectrum");
    plot(s[[i]], main="transformed (sqrt) and smoothed (ma5)");
    plot(b[[i]], main="baseline removed and peaks detected");
    points(p[[i]], pch=4, col=2);
}
par(mfrow=c(1, 1));