alsace (version 1.8.0)

getAllPeaks: 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)

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.

Value

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.

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")