averageMassSpectra-functions function

Averages MassSpectrum objects.

This function averages MassSpectrum objects.

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).

Details

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

Returns

Returns a single (no labels given) or a list

(labels given) of averaged MassSpectrum objects.

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

MassSpectrum, mergeMassPeaks

Website: https://strimmerlab.github.io/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")