Last data update: 2014.03.03

 R: Trim an AbstractMassObject object.
trim-methodsR Documentation

Trim an AbstractMassObject object.

Description

This method trims an AbstractMassObject object. That is useful if some mass ranges should be excluded from further analysis.

Usage

## S4 method for signature 'AbstractMassObject,numeric'
trim(object, range)
## S4 method for signature 'list,numeric'
trim(object, range, ...)
## S4 method for signature 'list,missing'
trim(object, range, ...)

Arguments

object

AbstractMassObject object or a list of AbstractMassObject objects.

range

numeric, limits of trimming (left/minimal mass, right/maximal mass). If missing it is automatically determined (largest overlapping mass range) for a list of AbstractMassObject.

...

arguments to be passed to underlying functions (currently only mc.cores is supported).

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

AbstractMassObject, MassPeaks, MassSpectrum

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

Examples

## load package
library("MALDIquant")

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

## select only one spectrum
s <- fiedler2009subset[[1]]

## remove all mass lower 3000
trim(s, range=c(3000, Inf))

## remove all mass higher 8000
trim(s, range=c(0, 8000))

## remove all mass lower 3000 and higher 8000
trim(s, range=c(3000, 8000))

## choose largest overlapping mass range for all spectra
trim(fiedler2009subset)

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/trim-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: trim-methods
> ### Title: Trim an AbstractMassObject object.
> ### Aliases: trim trim,AbstractMassObject,numeric-method
> ###   trim,list,numeric-method trim,list,missing-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> ## load package
> library("MALDIquant")
> 
> ## load example data
> data("fiedler2009subset", package="MALDIquant")
> 
> ## select only one spectrum
> s <- fiedler2009subset[[1]]
> 
> ## remove all mass lower 3000
> trim(s, range=c(3000, Inf))
S4 class type            : MassSpectrum                
Number of m/z values     : 28032                       
Range of m/z values      : 3000.146 - 9999.734         
Range of intensity values: 5 - 27518                   
Memory usage             : 337.133 KiB                 
Name                     : Pankreas_HB_L_061019_G10.M19
File                     : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m19/1/1SLin/fid
> 
> ## remove all mass higher 8000
> trim(s, range=c(0, 8000))
S4 class type            : MassSpectrum                
Number of m/z values     : 35846                       
Range of m/z values      : 1000.015 - 7999.732         
Range of intensity values: 124 - 101840                
Memory usage             : 428.703 KiB                 
Name                     : Pankreas_HB_L_061019_G10.M19
File                     : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m19/1/1SLin/fid
> 
> ## remove all mass lower 3000 and higher 8000
> trim(s, range=c(3000, 8000))
S4 class type            : MassSpectrum                
Number of m/z values     : 21490                       
Range of m/z values      : 3000.146 - 7999.732         
Range of intensity values: 124 - 27518                 
Memory usage             : 260.469 KiB                 
Name                     : Pankreas_HB_L_061019_G10.M19
File                     : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m19/1/1SLin/fid
> 
> ## choose largest overlapping mass range for all spectra
> trim(fiedler2009subset)
$sPankreas_HB_L_061019_G10.M19.T_0209513_0020740_18
S4 class type            : MassSpectrum                
Number of m/z values     : 42388                       
Range of m/z values      : 1000.015 - 9999.734         
Range of intensity values: 5 - 101840                  
Memory usage             : 505.367 KiB                 
Name                     : Pankreas_HB_L_061019_G10.M19
File                     : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m19/1/1SLin/fid

$sPankreas_HB_L_061019_G10.M20.T_0209513_0020740_18
S4 class type            : MassSpectrum                
Number of m/z values     : 42388                       
Range of m/z values      : 1000.015 - 9999.734         
Range of intensity values: 6 - 111862                  
Memory usage             : 505.367 KiB                 
Name                     : Pankreas_HB_L_061019_G10.M20
File                     : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m20/1/1SLin/fid

$sPankreas_HB_L_061019_H7.O14.T_0209513_0020740_18
S4 class type            : MassSpectrum               
Number of m/z values     : 42388                      
Range of m/z values      : 1000.015 - 9999.734        
Range of intensity values: 10 - 92807                 
Memory usage             : 505.367 KiB                
Name                     : Pankreas_HB_L_061019_H7.O14
File                     : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_H7/0_o14/1/1SLin/fid

$sPankreas_HB_L_061019_H7.P13.T_0209513_0020740_18
S4 class type            : MassSpectrum               
Number of m/z values     : 42388                      
Range of m/z values      : 1000.015 - 9999.734        
Range of intensity values: 3 - 94368                  
Memory usage             : 505.367 KiB                
Name                     : Pankreas_HB_L_061019_H7.P13
File                     : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_H7/0_p13/1/1SLin/fid

$sPankreas_HB_L_061019_F10.L19.T_0209513_0020740_18
S4 class type            : MassSpectrum                
Number of m/z values     : 42388                       
Range of m/z values      : 1000.015 - 9999.734         
Range of intensity values: 21 - 100220                 
Memory usage             : 505.367 KiB                 
Name                     : Pankreas_HB_L_061019_F10.L19
File                     : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F10/0_l19/1/1SLin/fid

$sPankreas_HB_L_061019_F10.L20.T_0209513_0020740_18
S4 class type            : MassSpectrum                
Number of m/z values     : 42388                       
Range of m/z values      : 1000.015 - 9999.734         
Range of intensity values: 8 - 87928                   
Memory usage             : 505.367 KiB                 
Name                     : Pankreas_HB_L_061019_F10.L20
File                     : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F10/0_l20/1/1SLin/fid

$sPankreas_HB_L_061019_F9.L17.T_0209513_0020740_18
S4 class type            : MassSpectrum               
Number of m/z values     : 42388                      
Range of m/z values      : 1000.015 - 9999.734        
Range of intensity values: 28 - 99022                 
Memory usage             : 505.367 KiB                
Name                     : Pankreas_HB_L_061019_F9.L17
File                     : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F9/0_l17/1/1SLin/fid

$sPankreas_HB_L_061019_F9.L18.T_0209513_0020740_18
S4 class type            : MassSpectrum               
Number of m/z values     : 42388                      
Range of m/z values      : 1000.015 - 9999.734        
Range of intensity values: 32 - 110268                
Memory usage             : 505.367 KiB                
Name                     : Pankreas_HB_L_061019_F9.L18
File                     : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F9/0_l18/1/1SLin/fid

$sPankreas_HB_L_061019_A6.A11.T_0209513_0020740_18
S4 class type            : MassSpectrum               
Number of m/z values     : 42388                      
Range of m/z values      : 1000.015 - 9999.734        
Range of intensity values: 23 - 61160                 
Memory usage             : 505.375 KiB                
Name                     : Pankreas_HB_L_061019_A6.A11
File                     : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A6/0_a11/1/1SLin/fid

$sPankreas_HB_L_061019_A6.A12.T_0209513_0020740_18
S4 class type            : MassSpectrum               
Number of m/z values     : 42388                      
Range of m/z values      : 1000.015 - 9999.734        
Range of intensity values: 46 - 54383                 
Memory usage             : 505.375 KiB                
Name                     : Pankreas_HB_L_061019_A6.A12
File                     : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A6/0_a12/1/1SLin/fid

$sPankreas_HB_L_061019_A8.A15.T_0209513_0020740_18
S4 class type            : MassSpectrum               
Number of m/z values     : 42388                      
Range of m/z values      : 1000.015 - 9999.734        
Range of intensity values: 36 - 84852                 
Memory usage             : 505.375 KiB                
Name                     : Pankreas_HB_L_061019_A8.A15
File                     : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A8/0_a15/1/1SLin/fid

$sPankreas_HB_L_061019_A8.A16.T_0209513_0020740_18
S4 class type            : MassSpectrum               
Number of m/z values     : 42388                      
Range of m/z values      : 1000.015 - 9999.734        
Range of intensity values: 75 - 86455                 
Memory usage             : 505.375 KiB                
Name                     : Pankreas_HB_L_061019_A8.A16
File                     : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A8/0_a16/1/1SLin/fid

$sPankreas_HB_L_061019_C4.F7.T_0209513_0020740_18
S4 class type            : MassSpectrum              
Number of m/z values     : 42388                     
Range of m/z values      : 1000.015 - 9999.734       
Range of intensity values: 15 - 23448                
Memory usage             : 505.375 KiB               
Name                     : Pankreas_HB_L_061019_C4.F7
File                     : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_C4/0_f7/1/1SLin/fid

$sPankreas_HB_L_061019_C4.F8.T_0209513_0020740_18
S4 class type            : MassSpectrum              
Number of m/z values     : 42388                     
Range of m/z values      : 1000.015 - 9999.734       
Range of intensity values: 36 - 30171                
Memory usage             : 505.375 KiB               
Name                     : Pankreas_HB_L_061019_C4.F8
File                     : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_C4/0_f8/1/1SLin/fid

$sPankreas_HB_L_061019_D9.G17.T_0209513_0020740_18
S4 class type            : MassSpectrum               
Number of m/z values     : 42388                      
Range of m/z values      : 1000.015 - 9999.734        
Range of intensity values: 8 - 32828                  
Memory usage             : 505.375 KiB                
Name                     : Pankreas_HB_L_061019_D9.G17
File                     : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_D9/0_g17/1/1SLin/fid

$sPankreas_HB_L_061019_D9.G18.T_0209513_0020740_18
S4 class type            : MassSpectrum               
Number of m/z values     : 42388                      
Range of m/z values      : 1000.015 - 9999.734        
Range of intensity values: 7 - 22786                  
Memory usage             : 505.375 KiB                
Name                     : Pankreas_HB_L_061019_D9.G18
File                     : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_D9/0_g18/1/1SLin/fid

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


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