MALDIquant (version 1.2)

mergeMassSpectra: Merges MassPeaks or MassSpectrum objects.

Description

These functions merge MassPeaks or MassSpectrum objects by a user defined function.

Usage

mergeMassPeaks(l, labels, fun=mean, ...)
mergeMassSpectra(l, labels, fun=mean, ...)

Arguments

l

list, list of MassPeaks or MassSpectrum objects.

labels

list, list of factors (one for each MassPeaks object) to do groupwise merging.

fun

used merge function (mean, median, sum or something else would be possible).

...

arguments to be passed to fun

Value

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

References

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

See Also

MassPeaks, MassSpectrum

Examples

## load library
library("MALDIquant");

## create four MassPeaks objects and add them to the list
p<- list(createMassPeaks(mass=1:2, intensity=1:2),
         createMassPeaks(mass=1:3, intensity=1:3),
         createMassPeaks(mass=1:4, intensity=1:4),
         createMassPeaks(mass=1:5, intensity=1:5))

## merge all four MassPeaks objects into a single new one 
## by sum their intensities
## (no labels, returns only one new MassPeaks object)
mergedPeaks <- mergeMassPeaks(p, fun=sum);

## compare result
mass(mergedPeaks)      # 1:5
intensity(mergedPeaks) # c(4, 8, 9, 8, 5) 

## only merge MassPeaks 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"));
mergedPeaks <- mergeMassPeaks(p, labels=groups, fun=sum);

## compare result
## group "a":
mass(mergedPeaks[[1]])      # 1:3
intensity(mergedPeaks[[1]]) # c(2, 4, 3)

## group "b":
mass(mergedPeaks[[2]])      # 1:5
intensity(mergedPeaks[[2]]) # c(2, 4, 6, 8, 5)