R: RDA Shrunken Gene List Function

genelist.rda {rda} | R Documentation

## RDA Shrunken Gene List Function

### Description

A function that returns the shrunken gene (variable) names by RDA for a particular (alpha, delta) combination.

### Usage

    genelist.rda(x, y, alpha, delta, prior=table(y)/length(y),
                 gnames=NULL, regularization="S")

### Arguments

`x` | The training data set for which you want to obtain the shrunken gene list. It must be a numerical matrix. The columns are sample observations and the rows are variables.
`y` | The class labels for the columns of 'x'.
`prior` | A numerical vector that gives the prior proportion of each class. By default, it is set to be the sample frequencies unless users want to specify a different one.
`alpha` | A single regularization value for alpha. Users must supply this option.
`delta` | A threshold value for delta. Users must supply this option.
`gnames` | A character vector that specifies the names of the variables of the training data set 'x'. By default, it is set to be `NULL` and the function uses either the row names of 'x' (if it exists) or the row index `1:nrow(x)`. Users can provide their customized gene name list. However, the length of the name vector must be the same as the number of rows of 'x'.
`regularization` | The type of regularization. It is either 'S' or 'R'. The default value is 'S'.

### Details

`genelist.rda` will return a vector of names for those shrunken genes by RDA for a particular (alpha, delta).

### Value

A character vector of the names of the shrunken genes.

### Author(s)

Yaqian Guo, Trevor Hastie and Robert Tibshirani

### References

Guo, Y. et al. (2004) Regularized Discriminant Analysis and Its Application in Microarrays, Technical Report, Department of Statistics, Stanford University.

### Examples

    data(colon)
    colon.x <- t(colon.x)
    genenames <- genelist.rda(colon.x, colon.y, alpha=0.1, delta=0.3)

[Package rda version 1.0.2-2.1 Index]