MALDIquant (version 0.3)

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 quantitative calibration and classification so that MALDIquant is useful for clinical diagnostics.

Details

ll{ Package: MALDIquant Version: 0.3 Date: 2011-05-28 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, function(x)transformIntensity(x, sqrt));

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

## smooth spectra
s <- lapply(t, function(x)transformIntensity(x, movingAvg));

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

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

## 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));