Smooths 'MSnExp' or 'Spectrum' instances

Description

This method smooths individual spectra (Spectrum instances) or whole experiments (MSnExp instances). Currently, the Savitzky-Golay-Smoothing (method = "SavitzkyGolay") and the Moving-Average-Smoothing (method = "MovingAverage") are available, as implemented in the MALDIquant::smoothIntensity function. Additional methods might be added at a later stage.

Methods

signature(x = "MSnExp", method = "character", halfWindowSize = "integer", verbose = "logical", ...)

Smooths all spectra in MSnExp. method could be "SavitzkyGolay" or "MovingAverage}. code{halfWindowSize} controls the window size of the filter. The resulting window size is code{2 * halfWindowSize + 1}. The best size differs depending on the selected code{method}. For code{method = "SavitzkyGolay"} it should be lower than emph{FWHM} of the peaks (full width at half maximum; please find details in Bromba and Ziegler 1981). The arguments code{dots} are passed to the internal functions. Currently the only supported argument is code{polynomialOrder} (default: 3) for code{method="SavitzkyGolay to control the polynomial order of the Savitzky-Golay Filter. This method displays a progress bar if verbose = TRUE. Returns an MSnExp instance with smoothed spectra.

signature(x = "Spectrum", method = "character", halfWindowSize = "integer", ...)

Smooths the spectrum (Spectrum instance). This method is the same as above but returns a smoothed Spectrum instead of an MSnExp object. It has no verbose argument. Please read the details for the above MSnExp method.

Author(s)

Sebastian Gibb <mail@sebastiangibb.de>

References

A. Savitzky and M. J. Golay. 1964. Smoothing and differentiation of data by simplified least squares procedures. Analytical chemistry, 36(8), 1627-1639.

M. U. Bromba and H. Ziegler. 1981. Application hints for Savitzky-Golay digital smoothing filters. Analytical Chemistry, 53(11), 1583-1586.

S. Gibb and K. Strimmer. 2012. MALDIquant: a versatile R package for the analysis of mass spectrometry data. Bioinformatics 28: 2270-2271. http://strimmerlab.org/software/maldiquant/

See Also

clean, pickPeaks, removePeaks and trimMz for other spectra processing methods.

Examples

sp1 <- new("Spectrum1",
           intensity = c(1:6, 5:1),
           mz = 1:11)
sp2 <- smooth(sp1, method = "MovingAverage", halfWindowSize = 2)
intensity(sp2)

data(itraqdata)
itraqdata2 <- smooth(itraqdata, 
                     method = "MovingAverage", 
                     halfWindowSize = 2)
processingData(itraqdata2)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(MSnbase)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 1.20.7 
  Read '?MSnbase' and references therein for information
  about the package and how to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:stats':

    smooth

The following object is masked from 'package:base':

    trimws

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MSnbase/smooth-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: smooth-methods
> ### Title: Smooths 'MSnExp' or 'Spectrum' instances
> ### Aliases: smooth-methods smooth
> ### Keywords: methods
> 
> ### ** Examples
> 
> sp1 <- new("Spectrum1",
+            intensity = c(1:6, 5:1),
+            mz = 1:11)
> sp2 <- smooth(sp1, method = "MovingAverage", halfWindowSize = 2)
> intensity(sp2)
 [1] 3.0 3.0 3.0 4.0 4.6 4.8 4.6 4.0 3.0 3.0 3.0
> 
> data(itraqdata)
> itraqdata2 <- smooth(itraqdata, 
+                      method = "MovingAverage", 
+                      halfWindowSize = 2)
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|======================================================================| 100%
> processingData(itraqdata2)
- - - Processing information - - -
Data loaded: Wed May 11 18:54:39 2011 
Spectra smoothed (MovingAverage): Wed Jul  6 01:10:50 2016 
 MSnbase version: 1.1.22 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>