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Last data update: 2014.03.03

R: Filter peak lists

filterPeaks

R Documentation

Filter peak lists

Description

Utility function to remove peaks from a peak list, e.g. because their intensity is too low. Currently one can filter on peak height, peak area, and width at half maximum.

Usage

filterPeaks(peakList, minHeight, minArea, minWHM, maxWHM)

Arguments

`peakList`	A nested list of peak tables: the first level is the sample, and the second level is the component. Every component is described by a matrix where every row is one peak, and the columns contain information on retention time, full width at half maximum (FWHM), peak width, height, and area.
`minHeight`	Minimum peak height.
`minArea`	Minimum peak area.
`minWHM`	Minimal width at half maximum.
`maxWHM`	Maximum width at half maximum.

Value

A peak list similar to the input peakList, but with all rows removed from the peak tables that are not satisfying the criteria.

Author(s)

Ron Wehrens

Examples

data(teaMerged)
pks <- getAllPeaks(teaMerged$CList, span = 11)
## only retain peaks with a peak height of at least 2
pks.filtered <- filterPeaks(pks, minHeight = 2)
plot(teaMerged, mat.idx = 3, what = "profiles", comp.idx = 2,
     showWindows = FALSE, col = "blue")
abline(v = pks[[3]][[2]][,"rt"], col = "gray", lty = 2)
abline(v = pks.filtered[[3]][[2]][,"rt"])

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)

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> library(alsace)
Loading required package: ALS
Loading required package: nnls
Loading required package: Iso
Iso 0.0-17
Loading required package: ptw
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/alsace/filterPeaks.Rd_%03d_medium.png", width=480, height=480)
> ### Name: filterPeaks
> ### Title: Filter peak lists
> ### Aliases: filterPeaks
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(teaMerged)
> pks <- getAllPeaks(teaMerged$CList, span = 11)
> ## only retain peaks with a peak height of at least 2
> pks.filtered <- filterPeaks(pks, minHeight = 2)
> plot(teaMerged, mat.idx = 3, what = "profiles", comp.idx = 2,
+      showWindows = FALSE, col = "blue")
> abline(v = pks[[3]][[2]][,"rt"], col = "gray", lty = 2)
> abline(v = pks.filtered[[3]][[2]][,"rt"])
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>