R: Robust PCA of a Spectra Object

r_pcaSpectra {ChemoSpec} | R Documentation

## Robust PCA of a Spectra Object

### 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

    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

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

[Package ChemoSpec version 4.4.97 Index]