r_pcaSpectra: Robust PCA of a Spectra Object

Description Usage Arguments Value Author(s) References See Also Examples

Description

A wrapper which carries out robust PCA analysis on a Spectra object. The data are row- and column-centered, and the user can select various options for scaling.

Usage

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r_pcaSpectra(spectra, choice = "noscale")

Arguments

spectra

An object of S3 class Spectra.

choice

A character vector describing the type of scaling to be carried out. One of c("noscale", "mad").

Value

An object of classes conPCA and princomp (see q2rPCA). It includes a list element called $method, a character string describing the pre-processing carried out and the type of PCA performed (it appears on plots which you might make).

Author(s)

Bryan A. Hanson, DePauw University.

References

K. Varmuza and P. Filzmoser Introduction to Multivariate Statistical Analysis in Chemometrics, CRC Press, 2009.

https://github.com/bryanhanson/ChemoSpec

See Also

See PCAgrid on which this function is based. For the classical version, see c_pcaSpectra.

For displaying the results, plotScree, plotScores, plotLoadings, plot2Loadings, sPlotSpectra, plotScores3D, plotScoresRGL.

Examples

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data(metMUD1)
pca <- r_pcaSpectra(metMUD1)
plotScores(metMUD1, pca, main = "metMUD1 NMR Data",
  pcs = c(1,2), ellipse = "cls", tol = 0.05)


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