Hierarchical Cluster-Based Peak Alignment on a Spectra Object

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, ...)

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.

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/

Author

Bryan A. Hanson (DePauw University).

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
}
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> 
#>  Spectrum 1 has 4 peaks
#>  Spectrum 2 has 4 peaks
#>  Spectrum 3 has 4 peaks
#>  Spectrum 4 has 4 peaks
#>  Spectrum 5 has 4 peaks
#>  Spectrum 6 has 4 peaks
#>  Spectrum 7 has 4 peaks
#>  Spectrum 8 has 4 peaks
#>  Spectrum 9 has 4 peaks
#>  Spectrum 10 has 4 peaks
#>  Spectrum 11 has 4 peaks
#>  Spectrum 12 has 4 peaks
#>  Spectrum 13 has 4 peaks
#>  Spectrum 14 has 4 peaks
#>  Spectrum 15 has 4 peaks
#>  Spectrum 16 has 4 peaks
#>  Spectrum 17 has 4 peaks
#>  Spectrum 18 has 4 peaks
#>  Spectrum 19 has 4 peaks
#>  Spectrum 20 has 4 peaks
#>  --------------------------------
#>  CluPA will run with maxShift= 100
#>  If you want CluPA automatically detect the optimal maxShift,
#>  let try with dohCluster(...,maxShift=NULL,..)
#>  --------------------------------
#> 
#>  aligning spectrum  1
#>  aligning spectrum  2
#>  aligning spectrum  3
#>  aligning spectrum  4
#>  aligning spectrum  5
#>  aligning spectrum  6
#>  aligning spectrum  7
#>  aligning spectrum  9
#>  aligning spectrum  10
#>  aligning spectrum  11
#>  aligning spectrum  12
#>  aligning spectrum  13
#>  aligning spectrum  14
#>  aligning spectrum  15
#>  aligning spectrum  16
#>  aligning spectrum  17
#>  aligning spectrum  18
#>  aligning spectrum  19
#>  aligning spectrum  20
#>  Median pearson correlation of aligned spectra: 0.9999948
#>  Alignment time:  6e-04  minutes
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.