clupaSpectra {ChemoSpec}

Hierarchical Cluster-Based Peak Alignment on a Spectra Object

Description

This function is a wrapper to several functions in the speaq package. It implements the CluPA algorithm described in the reference.

Usage

clupaSpectra(spectra, bT = NULL, ...)

Arguments

spectra

An object of S3 class Spectra().

bT

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.

Value

A modifed Spectra object.

Author(s)

Bryan A. Hanson (DePauw University).

References

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).

See Also

Additional documentation at https://bryanhanson.github.io/ChemoSpec/

Examples

# 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
}