MALDIquant (version 1.12)

referencePeaks: Creates a reference MassPeaks object.

Description

This function creates a reference MassPeaks object (also called Anchor Peaks) from a list of MassPeaks objects. Generally it is a combination of binPeaks and filterPeaks

Usage

referencePeaks(l, method=c("strict", "relaxed"), minFrequency=0.9,
               tolerance=0.002)

Arguments

l

list, list of MassPeaks objects.

method

bin creation rule (see binPeaks).

minFrequency

double, remove all peaks which occur in less than minFrequency*length(l) MassPeaks objects.

tolerance

double, maximal deviation of a peak position (mass) to be considered as identical.

Value

• Returns a new MassPeaks objects. The intensity slot of the returned MassPeaks represents the frequency of this mass position in all samples.

See Also

binPeaks, filterPeaks, MassPeaks

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

Examples

## load package
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))

## only use peaks which occur in all MassPeaks objects as reference peaks
refPeaks <- referencePeaks(p, minFrequency=1)

mass(refPeaks)      # 1:2
intensity(refPeaks) # c(1, 1)