R: Hierarchical Cluster-Based Peak Alignment on a Spectra Object

clupaSpectra {ChemoSpec} | R Documentation

## 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. hanson@depauw.edu

### 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).

https://github.com/bryanhanson/ChemoSpec

### Examples

    # July 2017: This function requires pkg speaq which in turn
    # requires pkg data.table, which is broken in the CRAN build
    # chain.  We make a check of the status so we can pass CRAN!

    if (requireNamespace("speaq", quietly = TRUE)) {

    data(alignMUD)

    plotSpectra(alignMUD, which = 1:20, lab.pos = 4.5, offset = 0.1,
      yrange = c(0, 1900), amp = 500, xlim = c(1.5, 1.8),
      main = "Misaligned NMR Spectra (alignMUD)")

    aMUD <- clupaSpectra(alignMUD)
    plotSpectra(aMUD, which = 1:20, lab.pos = 4.5, offset = 0.1,
      yrange = c(0, 1900), amp = 500, xlim = c(1.5, 1.8),
      main = "Aligned NMR Spectra (alignMUD)")

    } # end of namespace check

[Package ChemoSpec version 4.4.97 Index]