suppl: Projection of supplementary data onto axes from a between...
In SamGG/made4: Multivariate analysis of microarray data using ADE4

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

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

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

`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.

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 array2ade4. Use plot.bga to plot results from bga.

A list containing:

suppl

An object returned by suppl

Aedin Culhane

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

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

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)
}