suppl {made4} | R Documentation

## Projection of supplementary data onto axes from a between group analysis

### Description

Projection and class prediction of supplementary points onto axes from a between group analysis, `bga`.

### Usage

    suppl(dudi.bga, supdata, supvec = NULL, assign=TRUE, ...)
    ## S3 method for class 'suppl'
    plot(x, dudi.bga, axis1=1, axis2=2, supvec=x$true.class,
    supvec.pred= x$predicted, ...)

### Arguments

`dudi.bga` | An object returned by `bga`.
`supdata` | Test or blind dataset. Accepted formats are a `matrix`, `data.frame`, `ExpressionSet` or `marrayRaw-class`.
`supvec` | A factor or vector which describes the classes in the training dataset.
`supvec.pred` | A factor or vector which describes the classes which were predicted by `suppl`.
`assign` | A logical indicating whether class assignment should be calculated using the method described by Culhane et al., 2002. The default value is `TRUE`.
`x` | An object returned by `suppl`.
`axis1` | Integer, the column number for the x-axis. The default is 1.
`axis2` | Integer, the column number for the y-axis. The default is 2.
`...` | further arguments passed to or from other methods.

### Details

After performing a between group analysis on a training dataset using `bga`, a test dataset can be then projected onto `bga` axes using `suppl`.

`suppl` returns the projected coordinates and assignment of each test case (array).

The test dataset must contain the same number of variables (genes) as the training dataset. The input format of both the training dataset and test dataset are verified using `isDataFrame`. Use `plot.bga` to plot results from bga.

### Value

A list containing:

`suppl` | An object returned by `suppl`

### Author(s)

Aedin Culhane

### References

Culhane AC, et al., 2002 Between-group analysis of microarray data. Bioinformatics. 18(12):1600-8.

### See Also

See Also `bga`, `bca`, `plot.bga`, `bga.jackknife`

### Examples

    data(khan)
    #khan.bga<-bga(khan$train, khan$train.classes)
    if (require(ade4, quiet = TRUE)) {
    khan.bga<-bga.suppl(khan$train, supdata=khan$test, classvec=khan$train.classes,
              supvec=khan$test.classes)

    khan.bga
    plot.bga(khan.bga, genelabels=khan$annotation$Symbol)
    khan.bga$suppl

    plot.suppl(khan.bga$suppl, khan.bga)
    plot.suppl(khan.bga$suppl, khan.bga, supvec=NULL, supvec.pred=NULL)
    plot.suppl(khan.bga$suppl, khan.bga, axis1=2, axis2=3,supvec=NULL, supvec.pred=NULL)
    }

[Package made4 version 1.64.0 Index]