| suppl {made4} | R Documentation |
Projection and class prediction of supplementary points onto
axes from a between group analysis, bga.
suppl(dudi.bga, supdata, supvec = NULL, assign=TRUE, ...)
dudi.bga |
An object returned by bga |
supdata |
Test or blind dataset. Accepted formats are a matrix,
data.frame, exprSet or
marrayRaw |
supvec |
A factor or vector which describes the classes in the training dataset |
assign |
A logical indicating whether class assignment should be calculated using the method described by Culhane et al., 2002. The default value is TRUE |
... |
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,
between, 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
}