getAllPeaks {alsace} | R Documentation

## Extract all peaks from the chromatographic profiles of an ALS object

### Description

Extractor function to find all peaks in the chromatographic profiles of an ALS object. Peaks are located as local maxima within the given span (function `findpeaks`) and at the given positions a gaussian curve is fit (function `fitpeaks`).

### Usage

    getAllPeaks(CList, span = NULL, eps = 1e-01)

### Arguments

`CList` | A list of profile matrices, each of the same dimensions (timepoints times components).
`span` | The span used for identifying local maxima in the individual components. If not given, the default of `findpeaks` is used.
`eps` | Minimal value for the peak width, basically used to eliminate peaks with zero width.

### Value

The result is a list, with each element corresponding to one data file, and containing data for the fitted peaks for each of the ALS components. Note that this function presents the "rt", "sd" and "FWHM" fields in real time units.

### Author(s)

Ron Wehrens

### Examples

    data(teaMerged)
    pks <- getAllPeaks(teaMerged$CList, span = 11)
    ## show component 2 from the second file
    par(mfrow = c(2,1))
    plot(teaMerged, what = "profiles", showWindows = FALSE,
         mat.idx = 2, comp.idx = 2)
    ## and show where the peaks are picked
    abline(v = pks[[2]][[2]][,"rt"], col = "gray")

    ## same for component 6
    plot(teaMerged, what = "profiles", showWindows = FALSE,
         mat.idx = 2, comp.idx = 6, col = "red")
    abline(v = pks[[2]][[6]][,"rt"], col = "pink")

[Package alsace version 1.26.0 Index]