Trims 'MSnExp' or 'Spectrum' instances

Description

This method selects a range of MZ values in a single spectrum (Spectrum instances) or all the spectra of an experiment (MSnExp instances). The regions to trim are defined by the range of mzlim argument, such that MZ values < min(mzlim) and MZ values > max(mzlim) are trimmed away.

Methods

signature(object = "MSnExp", mzlim = "numeric")

Trims all spectra in MSnExp object according to mzlim. Returns a cleaned MSnExp instance.

signature(object = "Spectrum", mzlim = "numeric")

Trims the Spectrum object and retruns a new trimmed object.

Author(s)

Laurent Gatto <lg390@cam.ac.uk>

See Also

removePeaks and clean for other spectra processing methods.

Examples

mz <- 1:100
sp1 <- new("Spectrum2",
           mz=mz,
           intensity=abs(rnorm(length(mz))))
sp2 <- trimMz(sp1,c(25,75))
range(mz(sp1))
range(mz(sp2))

data(itraqdata)
itraqdata2 <- trimMz(itraqdata,c(113,117))
range(mz(itraqdata))
range(mz(itraqdata2))
processingData(itraqdata2)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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/trimMz-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: trimMz-methods
> ### Title: Trims 'MSnExp' or 'Spectrum' instances
> ### Aliases: trimMz-methods trimMz
> ### Keywords: methods
> 
> ### ** Examples
> 
> mz <- 1:100
> sp1 <- new("Spectrum2",
+            mz=mz,
+            intensity=abs(rnorm(length(mz))))
> sp2 <- trimMz(sp1,c(25,75))
> range(mz(sp1))
[1]   1 100
> range(mz(sp2))
[1] 25 75
> 
> data(itraqdata)
> itraqdata2 <- trimMz(itraqdata,c(113,117))
> range(mz(itraqdata))
[1]   99.99872 2069.27344
> range(mz(itraqdata2))
[1] 113.0459 116.7362
> processingData(itraqdata2)
- - - Processing information - - -
Data loaded: Wed May 11 18:54:39 2011 
MZ trimmed [113..117] 
 MSnbase version: 1.1.22 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>