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This function is a wrapper to several functions in the speaq package. It implements the CluPA algorithm described in the reference.
clupaSpectra(spectra, bT = NULL, ...)A modifed Spectra object.
An object of S3 class Spectra().
Numeric. The baseline threshold. Defaults to five percent of the
range of the data, in spectra$data. Passed to
detectSpecPeaks.
Other arguments to be passed to the underlying functions.
Bryan A. Hanson (DePauw University).
Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemiere F, Verschoren A, Goethals B, Laukens K. "An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data" BMC Bioinformatics vol. 12 pg. 405 (2011).
Additional documentation at https://bryanhanson.github.io/ChemoSpec/
# You need to install package speaq for this example
# This example assumes the graphics output is set to ggplot2 (see ?GraphicsOptions).
if (requireNamespace("speaq", quietly = TRUE)) {
library("ggplot2")
data(alignMUD)
p1 <- plotSpectra(alignMUD, which = 1:20, lab.pos = 4.5, offset = 0.1,
yrange = c(0, 5000), amp = 500)
p1 <- p1 + ggtitle("Misaligned NMR Spectra") +
coord_cartesian(xlim = c(1.5, 1.8), ylim = c(0, 1900))
p1
aMUD <- clupaSpectra(alignMUD)
p2 <- plotSpectra(aMUD, which = 1:20, lab.pos = 4.5, offset = 0.1,
yrange = c(0, 5000), amp = 500)
p2 <- p2 + ggtitle("Aligned NMR Spectra") +
coord_cartesian(xlim = c(1.5, 1.8), ylim = c(0, 1900))
p2
}
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