xval-methods {MLInterfaces} | R Documentation

## support for cross-validatory machine learning with ExpressionSets

### Description

support for cross-validatory machine learning with ExpressionSets

### Usage

    xval( data, classLab, proc, xvalMethod, group, indFun, niter,
    fsFun=NULL, fsNum=NULL, decreasing=TRUE, cluster=NULL, ... )
    balKfold(K)
    xvalML( formula, data, proc, xvalMethod="LOO", group, indFun, niter,
    fsFun=NULL, fsNum=10, decreasing=TRUE, cluster=NULL, ... )

### Arguments

`data` | instance of class `ExpressionSet`
`formula` | a model formula, typically with a dot on the RHS, and response variable chosen from `pData` columns.
`classLab` | character string identifying phenoData variable to label classifications
`proc` | an MLInterfaces method that returns an instance of `"classifOutput"`
`xvalMethod` | character string identifying cross-validation procedure to use: default is "LOO" (leave one out), alternatives are "LOG" (leave group out) and "FUN" (user-supplied partition extraction function, see Details below)
`group` | a vector (length equal to number of samples) enumerating groups for LOG xval method
`indFun` | a function that returns a set of indices to be saved as a test set; this function must have parameters `data`, `clab`, `iternum`; see Details
`niter` | number of iterations for user-specified partition function to be run
`fsFun` | function computing ranks of features for feature selection
`fsNum` | number of features to be kept for learning in each iteration
`decreasing` | logical, should be TRUE if `fsFun` provides high scores for high-performing features (e.g., is absolute value of a test statistics) and false if it provides low scores for high-performing features (e.g., p-value of a test).
`cluster` | NULL or an S4-class object with a defined `xvalLoop` method. Use this to execute `xval` on several nodes in a computer cluster. See documentation for `xvalLoop` for more information
`...` | arguments passed to the MLInterfaces generic `proc`
`K` | number of partitions to be used if `balKfold` is used as `indFun`

### Value

For fixed feature sets (`fsFun` not specified), a vector or matrix with length equal to the number of cross-validation assignments. Each element contains the label resulting from the cross-validation.
For dynamic feature sets (`fsFun` specified), a list with element `out` containing labels from cross-validations, and element `fs.memory` recording features used in each cross-validation.

### Details

NB: This is now regarded as a legacy approach. See `MLearn` for an approach in which the cross-validation specification is a parameter to MLearn.

If `xvalMethod` is `"FUN"`, then `indFun` must be a function with parameters `data`, `clab`, and `iternum`. This function returns indices that identify the training set for a given cross-validation iteration passed as the value of `iternum`. An example function is printed out when the example of this page is executed.

if `fsFun` is not `NULL`, then it must be a function with two arguments: the first can be transformed to a feature matrix (rows are objects, columns are features) and the second is a vector of class labels. The function returns a vector of scores, one for each object. The scores will be interpreted according to the value of `decreasing`, to select `fsNum` features. Thanks to Stephen Henderson of University College London for this functionality.

Note that if `fsFun` is non-null, then the RHS of `formula` will be ignored, and it is assumed that the RHS is ".". We will attempt to ameliorate this in a future revision. If you wish to subset the features in `data` before applying cross-validated feature selection, do this manually, not by specifying a nontrivial formula.

### Examples

    library(golubEsets)
    data(Golub_Merge)
    smallG <- Golub_Merge[200:250,]
    lk1 <- xval(smallG, "ALL.AML", knnB, xvalMethod="LOO", group=as.integer(0))
    table(lk1,smallG$ALL.AML)
    lk2 <- xval(smallG, "ALL.AML", knnB, xvalMethod="LOG", group=as.integer(
     rep(1:8,each=9)))
    table(lk2,smallG$ALL.AML)
    balKfold
    lk3 <- xval(smallG, "ALL.AML", knnB, xvalMethod="FUN", 0:0, indFun=balKfold(5), niter=5)
    table(lk3, smallG$ALL.AML)
    #
    # illustrate the xval FUN method in comparison to LOO
    #
    LOO2 <- xval(smallG, "ALL.AML", knnB, "FUN", 0:0, function(x,y,i) {
      (1:ncol(exprs(x)))[-i] }, niter=72 )
    table(lk1, LOO2)
    #
    # use Stephen Henderson's feature selection extensions
    #
    t.fun<-function(data, fac)
    {
            require(genefilter)
            # deal with the integer storage of golubTrain@exprs!
            xd <- matrix(as.double(exprs(data)), nrow=nrow(exprs(data)))
            return(abs(rowttests(xd,pData(data)[[fac]], tstatOnly=FALSE)$statistic))
    }
    lk3f <- xval(smallG, "ALL.AML", knnB, xvalMethod="LOO", 0:0, fsFun=t.fun)
    table(lk3f$out, smallG$ALL.AML)
    # use MLearn xval
    XXml = xvalML(ALL.AML~., smallG, "knn", "LOO")
    # show that it agrees with the fB approach
    table(XXml, lk1)
    # use MLearn xval with feature selection
    XXmlfs = xvalML(ALL.AML~., smallG, "knn", "LOO", fsFun=t.fun)
    # show that it agrees with the previous approach
    table(XXmlfs$out, lk3f$out)

[Package MLInterfaces version 1.14.1 Index]