Removes less frequent peaks.
This function removes infrequently occuring peaks in a list of
MassPeaks objects.
filterPeaks(l, minFrequency, minNumber, labels, mergeWhitelists=FALSE)
l |
|
minFrequency |
|
minNumber |
|
labels |
|
mergeWhitelists |
|
For mergeWhitelists=FALSE the filtering uses a separate peak whitelist
for each group specified by labels, and is done independently in each
group. For mergeWhitelists=TRUE the peak whitelists are combined,
which means that peaks that occur frequently in at least one group are also
kept in all other groups.
If both minFrequency and minNumber arguments are specified the
more stringent threshold is used.
Sebastian Gibb mail@sebastiangibb.de
## 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 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 objects 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 were removed in group "a"
filteredPeaks[groups == "a"]
## peaks at mass 5 were removed in group "b"
filteredPeaks[groups == "b"]
## only keep peaks which occur at least twice in a group
groups <- factor(c("a", "a", "b", "b", "b"), levels=c("a", "b"))
filteredPeaks <- filterPeaks(c(p, p[[3]]), minNumber=2, labels=groups)
## peaks at mass 3 were removed in group "a"
filteredPeaks[groups == "a"]
## peaks at mass 5 were removed in group "b"
filteredPeaks[groups == "b"]
## apply different minFrequency arguments to each group
groups <- factor(c("a", "a", "b", "b", "b"), levels=c("a", "b"))
filteredPeaks <- filterPeaks(c(p, p[[3]]), minFrequency=c(1, 2/3), labels=groups)
intensityMatrix(filteredPeaks)
# 1 2 3 4
#[1,] 1 2 NA NA
#[2,] 1 2 NA NA
#[3,] 1 2 3 4
#[4,] 1 2 3 4
#[4,] 1 2 3 4
## demonstrate the use of mergeWhitelists
groups <- factor(c("a", "a", "b", "b"), levels=c("a", "b"))
## default behaviour
filteredPeaks <- filterPeaks(p, minNumber=2, labels=groups)
intensityMatrix(filteredPeaks)
# 1 2 3 4
#[1,] 1 2 NA NA
#[2,] 1 2 NA NA
#[3,] 1 2 3 4
#[4,] 1 2 3 4
## use mergeWhitelists=TRUE to keep peaks of group "a" that match all filtering
## criteria in group "b"
## (please note that mass == 3 is not removed in the second MassPeaks object)
filteredPeaks <- filterPeaks(p, minNumber=2, labels=groups,
mergeWhitelists=TRUE)
intensityMatrix(filteredPeaks)
# 1 2 3 4
#[1,] 1 2 NA NA
#[2,] 1 2 3 NA
#[3,] 1 2 3 4
#[4,] 1 2 3 4Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.