pls_rfCMA {CMA} | R Documentation

## Partial Least Squares followed by random forests

### Description

This method constructs a classifier that extracts Partial Least Squares components used to generate Random Forests, s. `rfCMA`.

For `S4` method information, see `pls_rfCMA-methods`.

### Usage

    pls_rfCMA(X, y, f, learnind, comp = 2 * nlevels(as.factor(y)), seed = 111,models=FALSE, ...)

### Arguments

`X` | Gene expression data. Can be one of the following: A `matrix`. Rows correspond to observations, columns to variables. A `data.frame`, when `f` is not missing (s. below). An object of class `ExpressionSet`.
`y` | Class labels. Can be one of the following: A `numeric` vector. A `factor`. A `character` if `X` is an `ExpressionSet` that specifies the phenotype variable. `missing`, if `X` is a `data.frame` and a proper formula `f` is provided. WARNING: The class labels will be re-coded to range from `0` to `K-1`, where `K` is the total number of different classes in the learning set.
`f` | A two-sided formula, if `X` is a `data.frame`. The left part correspond to class labels, the right to variables.
`learnind` | An index vector specifying the observations that belong to the learning set. May be `missing`; in that case, the learning set consists of all observations and predictions are made on the learning set.
`comp` | Number of Partial Least Squares components to extract. Default ist two times the number of different classes.
`seed` | Fix Random number generator seed to `seed`. This is useful to guarantee reproducibility of the results, due to the random component in the random Forest.
`models` | a logical value indicating whether the model object shall be returned
`...` | Further arguments to be passed to `randomForests` from the package of the same name.

### Value

An object of class `cloutput`.

### Author(s)

Martin Slawski ms@cs.uni-sb.de

Anne-Laure Boulesteix boulesteix@ibe.med.uni-muenchen.de

### References

Boulesteix, A.L., Strimmer, K. (2007).

Partial least squares: a versatile tool for the analysis of high-dimensional genomic data.

Briefings in Bioinformatics 7:32-44.

### See Also

`compBoostCMA`, `dldaCMA`, `ElasticNetCMA`, `fdaCMA`, `flexdaCMA`, `gbmCMA`, `knnCMA`, `ldaCMA`, `LassoCMA`, `nnetCMA`, `pknnCMA`, `plrCMA`, `pls_ldaCMA`, `pls_lrCMA`, `pnnCMA`, `qdaCMA`, `rfCMA`, `scdaCMA`, `shrinkldaCMA`, `svmCMA`

### Examples

    ### load Golub AML/ALL data
    data(golub)
    ### extract class labels
    golubY <- golub[,1]
    ### extract gene expression
    golubX <- as.matrix(golub[,-1])
    ### select learningset
    ratio <- 2/3
    set.seed(111)
    learnind <- sample(length(golubY), size=floor(ratio*length(golubY)))
    ### run PLS, combined with Random Forest
    #result <- pls_rfCMA(X=golubX, y=golubY, learnind=learnind)
    ### show results
    #show(result)
    #ftable(result)
    #plot(result)

[Package CMA version 1.45.0 Index]