## load package
library("MALDIquant")
## create two MassPeaks objects
p <- list(createMassPeaks(mass=seq(100, 500, 100), intensity=1:5),
createMassPeaks(mass=c(seq(100.2, 300.2, 100), 395), intensity=1:4))
binnedPeaks <- binPeaks(p, tolerance=0.002)
## compare result
iM1 <- intensityMatrix(p)
iM2 <- intensityMatrix(binnedPeaks)
all(dim(iM1) == c(2, 9)) # TRUE
all(dim(iM2) == c(2, 6)) # TRUE
show(iM2)
## increase tolerance
binnedPeaks <- binPeaks(p, tolerance=0.1)
iM3 <- intensityMatrix(binnedPeaks)
all(dim(iM3) == c(2, 5)) # TRUE
show(iM3)
## differences between "strict" and "relaxed"
p <- c(createMassPeaks(mass=c(1, 1.01, 3), intensity=c(2, 1, 1)),
createMassPeaks(mass=c(0.99, 3), intensity=rep(1, 2)),
createMassPeaks(mass=c(1.02, 3), intensity=rep(1, 2)))
intensityMatrix(binPeaks(p, method="strict", tolerance=0.05))
intensityMatrix(binPeaks(p, method="relaxed", tolerance=0.05))
## use a reference
ref <- createMassPeaks(mass=c(1, 3), intensity=rep(1, 2))
## include the reference
intensityMatrix(binPeaks(c(ref, p), method="reference", tolerance=0.05))
## drop the reference
intensityMatrix(binPeaks(c(ref, p), method="reference", tolerance=0.05)[-1])
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