KBModelAccessors {kebabs} | R Documentation

## KBModel Accessors

### Description

KBModel Accessors

### Usage

    ## S4 method for signature 'KBModel'
    modelOffset(object)

    getSVMSlotValue(paramName, model, raw = FALSE)

### Arguments

`object` | a KeBABS model
`paramName` | unified name of an SVM model data element
`model` | a KeBABS model
`raw` | when set to `TRUE` the parameter value is delivered in exactly the way as it is stored in the SVM specific model, when set to `FALSE` it is delivered in unified format

### Value

`getSVMSlotValue`: value of requested parameter in unified or native format dependent on parameter `raw`.

### Accessor-like methods

  `modelOffset`: returns the model offset.

  `featureWeights`: returns the feature weights.

  `SVindex`: returns the support vector indices for the training samples.

  `cvResult`: returns result of cross validation as object of class `CrossValidationResult`.

  `modelSelResult`: returns result of model selection as object of class `ModelSelectionResult`.

  `svmModel`: returns the native svm model stored within KeBABS model.

  `probabilityModel`: returns the probability model stored within KeBABS model.

### Author(s)

Johannes Palme <kebabs@bioinf.jku.at>

### References

http://www.bioinf.jku.at/software/kebabs
J. Palme, S. Hochreiter, and U. Bodenhofer (2015) KeBABS: an R package for kernel-based analysis of biological sequences. Bioinformatics, 31(15):2574-2576, 2015. DOI: 10.1093/bioinformatics/btv176.

### Examples

    ## create kernel object for normalized spectrum kernel
    specK5 <- spectrumKernel(k=5)
    ## Not run:
    ## load data
    data(TFBS)

    ## perform training - feature weights are computed by default
    model <- kbsvm(enhancerFB, yFB, specK5, pkg="LiblineaR",
                   svm="C-svc", cost=15, cross=10, showProgress=TRUE)
                   showProgress=TRUE)

    ## show result of validation
    cvResult(model)
    ## show feature weights
    featureWeights(model)[1:5]
    ## show model offset
    modelOffset(model)

    ## End(Not run)

[Package kebabs version 1.21.0 Index]