Class "MassSpectrum"

Description

MassSpectrum represents a single spectrum of a MALDI-TOF mass spectrometry measurement. It provides an easy framework for doing some preprocessing steps like peak detection, baseline correction and much more.

Objects from the Class

createMassSpectrum: Creates a MassSpectrum object.

Extends

Class AbstractMassObject, directly.

Methods

calibrateIntensity

signature(x = "MassSpectrum"): Calibrates the intensity of a MassSpectrum object. See calibrateIntensity,MassSpectrum-method for details.

detectPeaks

signature(x = "MassSpectrum"): Look for local maxima and estimate noise to extract peaks out of a MassSpectrum object. See detectPeaks,MassSpectrum-method for details.

estimateBaseline

signature(x = "MassSpectrum"): Estimates the baseline of a MassSpectrum object. See estimateBaseline,MassSpectrum-method for details.

estimateNoise

signature(x = "MassSpectrum"): Estimates the noise of a MassSpectrum object. See estimateNoise,MassSpectrum-method for details.

isRegular

signature(object = "MassSpectrum"): Returns FALSE if the frequency of mass values with irregular intervals is greater than threshold (because object was measured in centroid mode or some intensity values were filtered).

removeBaseline

signature(x = "MassSpectrum"): Estimates and removes the baseline of a MassSpectrum object. See removeBaseline,MassSpectrum-method for details.

smoothIntensity

signature(object = "MassSpectrum"): Smoothes the intensities of an MassSpectrum object. See smoothIntensity,MassSpectrum-method for details.

totalIonCurrent

signature(object = "MassSpectrum"): Accessor function for Total Ion Current (TIC, area under the curve).

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

createMassSpectrum, calibrateIntensity,MassSpectrum-method, detectPeaks,MassSpectrum-method, estimateBaseline,MassSpectrum-method, estimateNoise,MassSpectrum-method, removeBaseline,MassSpectrum-method, smoothIntensity,MassSpectrum-method, AbstractMassObject

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

Examples

## load package
library("MALDIquant")

## create a MassSpectrum object by default constructor
s <- createMassSpectrum(mass=1:100, intensity=rnorm(100)^2,
                        metaData=list(name="example"))

## show some details
s

## plot spectrum
plot(s)

## get TIC
totalIonCurrent(s)

## modify intensity and metaData
intensity(s)[1:50] <- 0
metaData(s) <- list(name="modified example")

## plot again
plot(s)

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/MassSpectrum-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MassSpectrum-class
> ### Title: Class "MassSpectrum"
> ### Aliases: MassSpectrum MassSpectrum-class isRegular
> ###   isRegular,MassSpectrum-method totalIonCurrent
> ###   totalIonCurrent,MassSpectrum-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> ## load package
> library("MALDIquant")
> 
> ## create a MassSpectrum object by default constructor
> s <- createMassSpectrum(mass=1:100, intensity=rnorm(100)^2,
+                         metaData=list(name="example"))
> 
> ## show some details
> s
S4 class type            : MassSpectrum         
Number of m/z values     : 100                  
Range of m/z values      : 1 - 100              
Range of intensity values: 5.422e-05 - 9.177e+00
Memory usage             : 2.398 KiB            
Name                     : example              
> 
> ## plot spectrum
> plot(s)
> 
> ## get TIC
> totalIonCurrent(s)
[1] 115.2347
> 
> ## modify intensity and metaData
> intensity(s)[1:50] <- 0
> metaData(s) <- list(name="modified example")
> 
> ## plot again
> plot(s)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>