MALDIquant (version 1.6)

filterPeaks: Removes less frequently peaks.

Description

This function removes infrequently peaks from a list of MassPeaks objects.

Usage

filterPeaks(l, minFrequency, labels)

Arguments

l

list, list of MassPeaks objects.

minFrequency

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

labels

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

Value

• Returns a list of filtered MassPeaks objects.

References

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

See Also

intensityMatrix, MassPeaks

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))

## only keep peaks which occur in all MassPeaks objects
filteredPeaks <- filterPeaks(p, minFrequency=1)

## compare result
intensities <- intensityMatrix(filteredPeaks)

## peaks at mass 3,4,5 are removed
all(dim(intensities) == c(4, 2)) # TRUE
all(intensities[,1] == 1)        # TRUE
all(intensities[,2] == 2)        # TRUE

## only keep peaks which occur in all MassPeaks in a group
## (e.g. useful for technical replicates)
groups <- factor(c("a", "a", "b", "b"), levels=c("a", "b"))
filteredPeaks <- filterPeaks(p, minFrequency=1, labels=groups)

## peaks at mass 3 removed in group "a"
filteredPeaks[groups == "a"]

## peaks at mass 5 removed in group "b"
filteredPeaks[groups == "b"]