bga.suppl {made4} | R Documentation

## Between group analysis with supplementary data projection

### Description

`bga.suppl` performs a `bga` between group analysis with projection of supplementary points using `suppl`

### Usage

    bga.suppl(dataset, supdata, classvec, supvec = NULL, suponly = FALSE, type="coa", ...)

### Arguments

`dataset` | Training dataset. A `matrix`, `data.frame`, `ExpressionSet` or `marrayRaw-class`. 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`, `ExpressionSet` or `marrayRaw-class`. 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.
`type` | Character, "coa", "pca" or "nsc" indicating which data transformation is required. The default value is type="coa".
`...` | further arguments passed to or from other methods.

### Details

`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 `isDataFrame`. Use `plot.bga` to plot results from bga.

### Value

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 `bca`),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.

### 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`, `suppl`, `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
    }

[Package made4 version 1.64.0 Index]