| bga.suppl {made4} | R Documentation |
bga.suppl performs a bga between group analysis with projection
of supplementary points using suppl
bga.suppl(dataset, supdata, classvec, supvec = NULL, suponly = FALSE,...)
dataset |
Training dataset. A matrix, data.frame,
exprSet or marrayRaw.
If the input is gene expression data in a matrix or data.frame. The
rows and columns are expected to contain the variables (genes) and cases (array samples)
respectively.
|
supdata |
Test or blind dataset. A matrix, data.frame,
exprSet or marrayRaw.
If the input is gene expression data in a matrix or data.frame. The
rows and columns are expected to contain the variables (genes) and cases (array samples)
respectively. The test dataset supdata and the training dataset dataset must contain
the same number of variables (genes).
|
classvec |
A factor or vector which describes the classes in the
training data dataset |
supvec |
A factor or vector which describes the classes in the
test dataset supdata |
suponly |
Logical indicating whether the returned output should contain the test class assignment results only. The default value is FALSE, that is the training coordinates, test coordinates and class assignments will all be returned. |
... |
further arguments passed to or from other methods |
bga.suppl calls bga to perform between group analysis (bga) on the training dataset,
then it calls suppl to project the test dataset onto the bga axes.
It returns the coordinates and class assignment of the cases (microarray samples) in the test dataset as
described by Culhane et al., 2002.
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.
If suponly is FALSE (the default option) bga.suppl returns a list of length 4 containing
the results of the bga of the training dataset and the results of the projection of the test dataset onto the bga axes-
ord |
Results of initial ordination. A list of class "dudi" (see dudi). |
bet |
Results of between group analysis. A list of class "dudi"
(see dudi),"between" (see between),and
"dudi.bga"(see bga) |
fac |
The input classvec, the factor or vector which described the classes in the input dataset |
suppl |
An object returned by suppl |
If suponly is TRUE only the results from suppl will be returned.
Aedin Culhane
Culhane AC, et al., 2002 Between-group analysis of microarray data. Bioinformatics. 18(12):1600-8.
See Also bga,
suppl, 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
}