MALDIquant (version 1.18)

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

# NOT RUN {
## 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")
# }