# NOT RUN {
## load package
library("MALDIquant")
## load example data
data("fiedler2009subset", package="MALDIquant")
## choose only the first mass spectrum
s <- fiedler2009subset[[1]]
## SNIP
plot(s)
## estimate baseline
b <- estimateBaseline(s, method="SNIP", iterations=100)
## draw baseline on the plot
lines(b, col="red")
## TopHat
plot(s)
## estimate baseline (try different parameters)
b1 <- estimateBaseline(s, method="TopHat", halfWindowSize=75)
b2 <- estimateBaseline(s, method="TopHat", halfWindowSize=150)
## draw baselines on the plot
lines(b1, col=2)
lines(b2, col=3)
## draw legend
legend(x="topright", lwd=1, legend=paste0("halfWindowSize=", c(75, 150)),
col=c(2, 3))
## ConvexHull
plot(s)
## estimate baseline
b <- estimateBaseline(s, method="ConvexHull")
## draw baseline on the plot
lines(b, col="red")
## Median
plot(s)
## estimate baseline
b <- estimateBaseline(s, method="median")
## draw baseline on the plot
lines(b, col="red")
# }
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