GeneSelection {CMA} | R Documentation

## General method for variable selection with various methods

### Description

For different learning data sets as defined by the argument `learningsets`, this method ranks the genes from the most relevant to the less relevant using one of various 'filter' criteria or provides a sparse collection of variables (Lasso, ElasticNet, Boosting). The results are typically used for variable selection for the classification procedure that follows.
For S4 class information, s. `GeneSelection-methods`.

### Usage

    GeneSelection(X, y, f, learningsets, method = c("t.test", "welch.test", "wilcox.test", "f.test", "kruskal.test", "limma", "rfe", "rf", "lasso", "elasticnet", "boosting", "golub", "shrinkcat"), scheme, trace = TRUE, ...)

### 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`. `missing`, if `X` is a `data.frame` and a proper formula `f` is provided.
`f` | A two-sided formula, if `X` is a `data.frame`. The left part correspond to class labels, the right to variables.
`learningsets` | An object of class `learningsets`. May be missing, then the complete datasets is used as learning set.
`method` | A character specifying the method to be used: `t.test` two-sample t.test (equal variances for both classes assumed). `welch.test` Welch modification of the t.test (unequal variances for both classes). `wilcox.test` Wilcoxon rank sum test. `f.test` F test belonging to the linear hypothesis that the mean is the same for all classes. Usually used for the multiclass scheme, is equivalent to `method = t.test` in the two-class case. `kruskal.test` Multi-class generalization of the Wilcoxon rank sum test and the nonparametric pendant to the F test, respectively. `limma` 'Moderated t' statistic for the two-class case and 'moderated F' statistic for the multiclass case, described in Smyth (2003). Requires the package `limma`. `rfe` One-step Recursive Feature Elimination, based on the Support Vector Machine. The method is decribed in Guyon et al. (2002). Requires the package `e1071`. Take care that appropriate hyperparameters are passed by the `...` argument. `rf` Random Forest Variable Importance Measure. Requires the package `randomForest` `lasso` `L1` penalized logistic regression leads to sparsity with respect to the variables used. Calls the function `LassoCMA`, which requires the package `glmpath`. warning: Take care that appropriate hyperparameters are passed by the `...` argument. `elasticnet` Penalized logistic regression with both `L1` and `L2` penalty, claimed by Zhou and Hastie (2004) to select 'variable groups'. Calls the function `ElasticNetCMA`, which requires the package `glmpath`. warning: Take care that appropriate hyperparameters are passed by the `...` argument. `boosting` Componentwise boosting (Buehlmann and Yu, 2003) has been shown to mimic the LASSO (Efron et al., 2004; Buehlmann and Yu, 2006). Calls the function `compBoostCMA` Take care that appropriate hyperparameters are passed by the `...` argument. `golub` The (theoretically unfounded) variable selection criterion used by Golub et al. (1999), s. `golub`. `shrinkcat` The correlation-adjusted t-score from Zuber and Strimmer (2009)
`scheme` | The scheme to be used in the case of a non-binary response. Must be one of `"pairwise"`,`"one-vs-all"` or `"multiclass"`. The last case only makes sense if `method` is one of `f.test, limma, rf, boosting`, which can directly be applied to the multi class case.
`trace` | Should the progress be traced ? Default is `TRUE`.
`...` | Further arguments passed to the function performing variable selection, s. `method`.

### Value

An object of class `genesel`.

### Note

most of the methods described above are only apt for the binary classification case. The only ones that can be used without restriction in the multiclass case are

- `f.test`

- `kruskal.test`

- `rf`

- `boosting`

For the rest, pairwise or one-vs-all schemes are used.

### Author(s)

Martin Slawski ms@cs.uni-sb.de

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

Christoph Bernau bernau@ibe.med.uni-muenchen.de

### References

Smyth, G. K., Yang, Y.-H., Speed, T. P. (2003).
Statistical issues in microarray data analysis.
Methods in Molecular Biology 224, 111-136.

Guyon, I., Weston, J., Barnhill, S., Vapnik, V. (2002).
Gene Selection for Cancer Classification using support vector machines. Journal of Machine Learning Research, 46, 389-422

Zhou, H., Hastie, T. (2004).
Regularization and variable selection via the elastic net. Journal of the Royal Statistical Society B, 67(2),301-320

Buelmann, P., Yu, B. (2003).
Boosting with the L2 loss: Regression and Classification.
Journal of the American Statistical Association, 98, 324-339

Efron, B., Hastie, T., Johnstone, I., Tibshirani, R. (2004).
Least Angle Regression.
Annals of Statistics, 32:407-499

Buehlmann, P., Yu, B. (2006).
Sparse Boosting.
Journal of Machine Learning Research, 7- 1001:1024

Slawski, M. Daumer, M. Boulesteix, A.-L. (2008) CMA - A comprehensive Bioconductor package for supervised classification with high dimensional data. BMC Bioinformatics 9: 439

### See Also

`filter`, `GenerateLearningsets`, `tune`, `classification`

### Examples

    # load Golub AML/ALL data
    data(golub)
    ### extract class labels
    golubY <- golub[,1]
    ### extract gene expression from first 10 genes
    golubX <- as.matrix(golub[,-1])
    ### Generate five different learningsets
    set.seed(111)
    five <- GenerateLearningsets(y=golubY, method = "CV", fold = 5, strat = TRUE)
    ### simple t-test:
    selttest <- GeneSelection(golubX, golubY, learningsets = five, method = "t.test")
    ### show result:
    show(selttest)
    toplist(selttest, k = 10, iter = 1)
    plot(selttest, iter = 1)

[Package CMA version 1.38.0 Index]