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MALDIquant (version 1.18)

removeBaseline-methods: Removes the baseline of a MassSpectrum object.

Description

This method removes the baseline of mass spectrometry data (represented by a '>MassSpectrum object). The intensity of the mass spectrometry data would be reduced by baseline.

Usage

# S4 method for MassSpectrum
removeBaseline(object,
  method=c("SNIP", "TopHat", "ConvexHull", "median"),
  …)
# S4 method for list
removeBaseline(object, …)

Arguments

object

'>MassSpectrum object or a list of '>MassSpectrum objects.

method

used baseline estimation method, one of "SNIP", "TopHat", "ConvexHull" or "median". See estimateBaseline,MassSpectrum-method for details.

arguments to be passed to estimateBaseline,MassSpectrum-method. If object is a list mc.cores is also supported.

Value

Returns a modified '>MassSpectrum object with reduced intensities.

See Also

'>MassSpectrum, estimateBaseline,MassSpectrum-method

demo("baseline")

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

Examples

Run this code
# NOT RUN {
## load package
library("MALDIquant")

## load example data
data("fiedler2009subset", package="MALDIquant")

## choose only the first mass spectrum
s <- fiedler2009subset[[1]]

## plot spectrum
plot(s)

## subtract baseline
b <- removeBaseline(s, method="SNIP")

## draw modified spectrum on the plot
lines(b, col="blue")
# }

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