Transforms intensities of an AbstractMassObject object.

Description

This method performs a transformation (e.g. sqrt-transformation) on the intensities of an AbstractMassObject object.

Usage

## S4 method for signature 'AbstractMassObject'
transformIntensity(object,
  method=c("sqrt", "log", "log2", "log10"))
## S4 method for signature 'list'
transformIntensity(object, ...)

Arguments

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

AbstractMassObject, MassSpectrum

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

Examples

## load package
library("MALDIquant")

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

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

## transform spectrum
t <- transformIntensity(s, method="sqrt")

## plot spectrum
par(mfrow=c(2, 1))
plot(s, main="raw spectrum")
plot(t, main="transformed spectrum")
par(mfrow=c(1, 1))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MALDIquant)

This is MALDIquant version 1.15
Quantitative Analysis of Mass Spectrometry Data
 See '?MALDIquant' for more information about this package.

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MALDIquant/transformIntensity-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: transformIntensity-methods
> ### Title: Transforms intensities of an AbstractMassObject object.
> ### Aliases: transformIntensity
> ###   transformIntensity,AbstractMassObject-method
> ###   transformIntensity,list-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> ## load package
> library("MALDIquant")
> 
> ## load example data
> data("fiedler2009subset", package="MALDIquant")
> 
> ## choose only the first mass spectrum
> s <- fiedler2009subset[[1]]
> 
> ## transform spectrum
> t <- transformIntensity(s, method="sqrt")
> 
> ## plot spectrum
> par(mfrow=c(2, 1))
> plot(s, main="raw spectrum")
> plot(t, main="transformed spectrum")
> par(mfrow=c(1, 1))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>