MALDIquant (version 1.12)

averageMassSpectra: Averages MassSpectrum objects.

Description

This function averages MassSpectrum objects.

Usage

averageMassSpectra(l, labels, method=c("mean", "median", "sum"), ...)

Arguments

l

list, list of MassSpectrum objects.

labels

list, list of factors (one for each MassSpectrum object) to do groupwise averaging.

method

used aggregation function.

...

arguments to be passed to underlying functions (currently only mc.cores is supported).

Value

• Returns a single (no labels given) or a list (labels given) of averaged MassSpectrum objects.

Details

The mass of the averaged MassSpectrum object will be the mass of the first non-empty MassSpectrum object (of each group).

See Also

MassSpectrum, mergeMassPeaks

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

Examples

## load package
library("MALDIquant")

## create four MassSpectrum objects and add them to a list
s <- list(createMassSpectrum(mass=1:5, intensity=1:5),
          createMassSpectrum(mass=1:5, intensity=1:5),
          createMassSpectrum(mass=1:5, intensity=6:10),
          createMassSpectrum(mass=1:5, intensity=6:10))

## average all four MassSpectrum objects into a single new one
## by sum their intensities
## (no labels, returns only one new MassSpectrum object)
summedSpectra <- averageMassSpectra(s, method="sum")

## only average MassSpectrum objects in a group
## (e.g. useful for technical replicates)
## (two different labels, returns a list of two new MassPeaks objects)
groups <- factor(c("a", "a", "b", "b"), levels=c("a", "b"))
averagedSpectra <- averageMassSpectra(s, labels=groups, method="mean")