removeBaseline-methods {MALDIquant}

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 signature 'MassSpectrum'
removeBaseline(object,
  method=c("SNIP", "TopHat", "ConvexHull", "median"),
  ...)
## S4 method for signature '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.

Author(s)

Sebastian Gibb [e-mail]

See Also

MassSpectrum, estimateBaseline,MassSpectrum-method

demo("baseline")

Website: https://strimmerlab.github.io/software/maldiquant/

Examples

## 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")