ModelSelectionResultAccessors: ModelSelectionResult Accessors
In kebabs: Kernel-Based Analysis Of Biological Sequences

Description Usage Arguments Value Accessor-like methods Author(s) References Examples

ModelSelectionResult Accessors

1 2	## S4 method for signature 'ModelSelectionResult' gridRows(object)

object

a model selection result object (can be extracted from KeBABS model with accessor modelSelResult)

gridRows: returns a list of kernel objects
gridColumns: returns a DataFrame object with grid column parameters
gridErrors: returns a matrix with grid errors
performance: returns a list of matrices with performance values selGridRow: returns the selected kernel selGridCol: returns the selected SVM and/or hyperparameter(s) fullModel: returns a kebabs model of class KBModel

: gridRows: return the grid rows containing the kernels.
: gridColumns: return the grid columns.
: gridErrors: return the grid CV errors.
: performance: return the collected performance parameters.
: selGridRow: return the selected grid row.
: selGridCol: return the selected grid column.
: fullModel: return the full model.

Johannes Palme <kebabs@bioinf.jku.at>

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.

## 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=c(1,15,50,100), cross=10,
               perfParameters="ALL", showProgress=TRUE)

## show model selection result
mres <- modelSelResult(model)
mres

## extract grid errors
gridErrors(mres)

## extract other performance parameters
performance(mres)

## End(Not run)