evaluateParameters {macat} | R Documentation

## Evaluate Performance of Kernel Parameters by Cross-validation

### Description

For a given data set, chromosome, class, and kernel function, this function helps in determining optimal settings for the kernel parameter(s). The performance of individual parameter setting is assessed by cross- validation.

### Usage

    evaluateParameters(data, class, chromosome, kernel, kernelparams = NULL,
                       paramMultipliers = 2^(-4:4), subset = NULL,
                       newlabels = NULL, ncross = 10, verbose = TRUE)

### Arguments

`data` | Gene expression data in the MACAT list format. See data(stjude) for an example.
`class` | Sample class to be analyzed
`chromosome` | Chromosome to be analyzed
`kernel` | Choose kernel to smooth scores along the chromose. Available are 'kNN' for k-Nearest-Neighbors, 'rbf' for radial-basis-function (Gaussian), 'basePairDistance' for a kernel, which averages over all genes within a given range of base pairs around a position.
`kernelparams` | Additional parameters for the kernel as list, e.g., kernelparams=list(k=5) for taking the 5 nearest neighbours in the kNN-kernel. If NULL some defaults are set within the function.
`paramMultipliers` | Numeric vector. If you do cross-validation of the kernel parameters, specify these as multipliers of the given (standard) kernel parameter, depending on your kernel choice (see page 5 of the vignette). The multiplication results are the kernel argument settings, among which you want to search for the optimal one using cross-validation.
`subset` | If a subset of samples is to be used, give vector of column- indices of these samples in the original matrix here.
`newlabels` | If other labels than the ones in the MACAT-list-structure are to be used, give them as character vector/factor here. Make sure argument 'class' is one of them.
`ncross` | Integer. Specify how many folds in cross-validation.
`verbose` | Logical. Should progress be reported to STDOUT?

### Value

A list of class 'MACATevP' with 4 components:

`[parameterName]` | List of assessed settings for the parameter [parameterName].
`avgResid` | Average Residual Sum of Suares for the parameter settings in the same order as the first component.
`multiplier` | Multiplier of the original parameters in the same order as the first components.
`best` | List of parameter settings considered optimal by cross- validation. Can be directly inserted under the argument 'kernelparams' of the 'evalScoring' function.

### Author(s)

MACAT development team

### See Also

`evalScoring`

### Examples

    data(stjd)
    evalkNN6 <- evaluateParameters(stjd, class="T", chromosome=6,kernel=kNN,
                                   paramMultipliers=c(0.01,seq(0.2,2.0,0.2),2.5))
    plot(evalkNN6)

[Package macat version 1.10.0 Index]