MALDIquant: removeBaseline-methods – R documentation

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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 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 mail@sebastiangibb.de

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")

MALDIquant

Quantitative Analysis of Mass Spectrometry Data

v1.19.3

GPL (>= 3)

Authors

Sebastian Gibb [aut, cre] (<https://orcid.org/0000-0001-7406-4443>), Korbinian Strimmer [ths] (<https://orcid.org/0000-0001-7917-2056>)

Initial release

2019-05-12