# Kernel-Based Analysis of Biological Sequences

## Documentation for package ‘kebabs’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I K L M N P R S T W Y misc

## -- A --

AAVector | DNAVector, RNAVector, AAVector Objects and BioVector Class
AAVector-class | BioVector, DNAVector, RNAVector and AAVector Classes
annotationCharset | Annotation Specific Kernel
annotationCharset-method | Annotation Specific Kernel
annotationMetadata | Annotation Specific Kernel
annotationMetadata-method | Annotation Specific Kernel
annotationMetadata<- | Annotation Specific Kernel
annotationMetadata<--method | Annotation Specific Kernel
AnnotationSpecificKernel | Annotation Specific Kernel
annotationSpecificKernel | Annotation Specific Kernel
as.character-method | DNAVector, RNAVector, AAVector Objects and BioVector Class
as.KernelMatrix | KernelMatrix Accessors
as.KernelMatrix-method | KernelMatrix Accessors
auc | ROCData Accessors
auc-method | ROCData Accessors
auc<- | ROCData Accessors
auc<--method | ROCData Accessors

## -- B --

baselines | PredictionProfile Accessors
baselines-method | PredictionProfile Accessors
BioVector | DNAVector, RNAVector, AAVector Objects and BioVector Class
BioVector-class | BioVector, DNAVector, RNAVector and AAVector Classes

## -- C --

c-method | DNAVector, RNAVector, AAVector Objects and BioVector Class
ccannot | KeBABS Sequence Data
ccgroups | KeBABS Sequence Data
ccseq | KeBABS Sequence Data
character | Annotation Specific Kernel
class:AAVector | BioVector, DNAVector, RNAVector and AAVector Classes
class:BioVector | BioVector, DNAVector, RNAVector and AAVector Classes
class:ControlInformation | KeBABS Control Information Class
class:CrossValidationResult | Cross Validation Result Class
class:DNAVector | BioVector, DNAVector, RNAVector and AAVector Classes
class:ExplicitRepresentation | Explicit Representation Dense and Sparse Classes
class:ExplicitRepresentationDense | Explicit Representation Dense and Sparse Classes
class:ExplicitRepresentationSparse | Explicit Representation Dense and Sparse Classes
class:GappyPairKernel | Gappy Pair Kernel Class
class:KBModel | KeBABS Model Class
class:KernelMatrix | Kernel Matrix Class
class:MismatchKernel | Mismatch Kernel Class
class:ModelSelectionResult | Model Selection Result Class
class:MotifKernel | Motif Kernel Class
class:PredictionProfile | Prediction Profile Class
class:RNAVector | BioVector, DNAVector, RNAVector and AAVector Classes
class:ROCData | ROC Data Class
class:SequenceKernel | Sequence Kernel Class
class:SpectrumKernel | Spectrum Kernel Class
class:SVMInformation | SVM Information Class
class:SymmetricPairKernel | Symmetric Pair Kernel Class
computeROCandAUC | Compute Receiver Operating Characteristic And Area Under The Curve
ControlInformation | KeBABS Control Information Class
ControlInformation-class | KeBABS Control Information Class
cross.validation | KeBABS Cross Validation
CrossValidation | KeBABS Cross Validation
crossValidation | KeBABS Cross Validation
CrossValidationResult | Cross Validation Result Class
CrossValidationResult-class | Cross Validation Result Class
CrossValidationResultAccessors | CrossValidationResult Accessors
cvResult | KBModel Accessors
cvResult-method | KBModel Accessors
cvResult<- | KBModel Accessors
cvResult<--method | KBModel Accessors

## -- D --

DistanceWeightedKernel | Position Dependent Kernel
distanceWeightedKernel | Position Dependent Kernel
DNAVector | DNAVector, RNAVector, AAVector Objects and BioVector Class
DNAVector-class | BioVector, DNAVector, RNAVector and AAVector Classes

## -- E --

enhancerFB | KeBABS Sequence Data
evaluatePrediction | Evaluate Prediction
ExplicitRepresentation | Explicit Representation Dense and Sparse Classes
ExplicitRepresentation-class | Explicit Representation Dense and Sparse Classes
ExplicitRepresentationAccessors | ExplicitRepresentation Accessors
ExplicitRepresentationDense | Explicit Representation Dense and Sparse Classes
ExplicitRepresentationDense-class | Explicit Representation Dense and Sparse Classes
ExplicitRepresentationSparse | Explicit Representation Dense and Sparse Classes
ExplicitRepresentationSparse-class | Explicit Representation Dense and Sparse Classes
expWeight | Position Dependent Kernel

## -- F --

featureWeights | KBModel Accessors
featureWeights-method | KBModel Accessors
featureWeights<- | KBModel Accessors
featureWeights<--method | KBModel Accessors
folds | CrossValidationResult Accessors
folds-method | CrossValidationResult Accessors
fpr | ROCData Accessors
fpr-method | ROCData Accessors
fpr<- | ROCData Accessors
fpr<--method | ROCData Accessors
fullModel | ModelSelectionResult Accessors
fullModel-method | ModelSelectionResult Accessors

## -- G --

GappyPairKernel | Gappy Pair Kernel Class
gappyPairKernel | Gappy Pair Kernel
GappyPairKernel-class | Gappy Pair Kernel Class
gaussWeight | Position Dependent Kernel
genRandBioSeqs | Generate Random Biological Sequences
getExRep | Explict Representation
getExRepQuadratic | Explict Representation
getFeatureSpaceDimension | Spectrum Kernel
getFeatureSpaceDimension-method | Gappy Pair Kernel
getFeatureSpaceDimension-method | Mismatch Kernel
getFeatureSpaceDimension-method | Motif Kernel
getFeatureSpaceDimension-method | Spectrum Kernel
getFeatureWeights | Feature Weights
getKernelMatrix | Sequence Kernel
getPredictionProfile | Calculation Of Predicition Profiles
getPredictionProfile-method | Calculation Of Predicition Profiles
getPredProfMixture | Calculation Of Predicition Profiles for Mixture Kernels
getPredProfMixture-method | Calculation Of Predicition Profiles for Mixture Kernels
getSVMSlotValue | KBModel Accessors
grid.search | KeBABS Grid Search
gridColumns | ModelSelectionResult Accessors
gridColumns-method | ModelSelectionResult Accessors
gridErrors | ModelSelectionResult Accessors
gridErrors-method | ModelSelectionResult Accessors
gridRows | ModelSelectionResult Accessors
gridRows-method | ModelSelectionResult Accessors
GridSearch | KeBABS Grid Search
gridSearch | KeBABS Grid Search

## -- H --

heatmap | Heatmap Methods
heatmap-method | Heatmap Methods

## -- I --

isUserDefined | Sequence Kernel
isUserDefined-method | Sequence Kernel

## -- K --

KBModel | KeBABS Model Class
KBModel-class | KeBABS Model Class
KBModelAccessors | KBModel Accessors
kbsvm | KeBABS Training Methods
kbsvm-method | KeBABS Training Methods
KEBABS | kebabs
KeBABS | kebabs
kebabs | kebabs
kebabsCollectInfo | Collect KeBABS Package Information
kebabsData | KeBABS Sequence Data
kebabsDemo | kebabs
KernelMatrix | Kernel Matrix Class
KernelMatrix-class | Kernel Matrix Class
KernelMatrixAccessors | KernelMatrix Accessors
kernelParameters | Sequence Kernel
kernelParameters-method | Sequence Kernel

## -- L --

length | DNAVector, RNAVector, AAVector Objects and BioVector Class
length-method | DNAVector, RNAVector, AAVector Objects and BioVector Class
linearKernel | Linear Kernel
linWeight | Position Dependent Kernel

## -- M --

MismatchKernel | Mismatch Kernel Class
mismatchKernel | Mismatch Kernel
MismatchKernel-class | Mismatch Kernel Class
model.selection | KeBABS Model Selection
modelOffset | KBModel Accessors
modelOffset-method | KBModel Accessors
modelOffset<- | KBModel Accessors
modelOffset<--method | KBModel Accessors
ModelSelection | KeBABS Model Selection
modelSelection | KeBABS Model Selection
ModelSelectionResult | Model Selection Result Class
ModelSelectionResult-class | Model Selection Result Class
ModelSelectionResultAccessors | ModelSelectionResult Accessors
modelSelResult | KBModel Accessors
modelSelResult-method | KBModel Accessors
modelSelResult<- | KBModel Accessors
modelSelResult<--method | KBModel Accessors
MotifKernel | Motif Kernel Class
motifKernel | Motif Kernel
MotifKernel-class | Motif Kernel Class

## -- N --

names | DNAVector, RNAVector, AAVector Objects and BioVector Class
names-method | DNAVector, RNAVector, AAVector Objects and BioVector Class
names<- | DNAVector, RNAVector, AAVector Objects and BioVector Class
names<--method | DNAVector, RNAVector, AAVector Objects and BioVector Class

## -- P --

performance | ModelSelectionResult Accessors
performance-method | CrossValidationResult Accessors
performance-method | ModelSelectionResult Accessors
performCrossValidation | KeBABS Cross Validation
performCrossValidation-method | KeBABS Cross Validation
performGridSearch | KeBABS Grid Search
performModelSelection | KeBABS Model Selection
plot | Plot Prediction Profiles, Cross Validation Result, Grid Search Performance Parameters and Receiver Operating Characteristics
plot-method | Plot Prediction Profiles, Cross Validation Result, Grid Search Performance Parameters and Receiver Operating Characteristics
PositionDependentKernel | Position Dependent Kernel
positionDependentKernel | Position Dependent Kernel
positionMetadata | Position Dependent Kernel
positionMetadata-method | Position Dependent Kernel
positionMetadata<- | Position Dependent Kernel
positionMetadata<--method | Position Dependent Kernel
PositionSpecificKernel | Position Dependent Kernel
positionSpecificKernel | Position Dependent Kernel
predict | KeBABS Prediction Methods
predict-method | KeBABS Prediction Methods
predict.KBModel | KeBABS Prediction Methods
predict.kbsvm | KeBABS Prediction Methods
PredictionProfile | Prediction Profile Class
PredictionProfile-class | Prediction Profile Class
PredictionProfileAccessors | PredictionProfile Accessors
predictSVM | SVM Access for Training and Prediction
predictSVM-method | SVM Access for Training and Prediction
predictSVM.KernelMatrix | SVM Access for Training and Prediction
probabilityModel | KBModel Accessors
probabilityModel-method | KBModel Accessors
probabilityModel<- | KBModel Accessors
probabilityModel<--method | KBModel Accessors
profiles | PredictionProfile Accessors
profiles-method | PredictionProfile Accessors

## -- R --

RNAVector | DNAVector, RNAVector, AAVector Objects and BioVector Class
RNAVector-class | BioVector, DNAVector, RNAVector and AAVector Classes
ROCData | ROC Data Class
ROCData-class | ROC Data Class
ROCDataAccessors | ROCData Accessors

## -- S --

selGridCol | ModelSelectionResult Accessors
selGridCol-method | ModelSelectionResult Accessors
selGridRow | ModelSelectionResult Accessors
selGridRow-method | ModelSelectionResult Accessors
seqKernelAsChar | Sequence Kernel
SequenceKernel | Sequence Kernel Class
sequenceKernel | Sequence Kernel
SequenceKernel-class | Sequence Kernel Class
sequences | PredictionProfile Accessors
sequences-method | PredictionProfile Accessors
set | Annotation Specific Kernel
show | Display Various KeBABS Objects
show-method | Display Various KeBABS Objects
show.BioVector | Display Various KeBABS Objects
showAnnotatedSeq | Annotation Specific Kernel
SpectrumKernel | Spectrum Kernel Class
spectrumKernel | Spectrum Kernel
SpectrumKernel-class | Spectrum Kernel Class
SVindex | KBModel Accessors
SVindex-method | KBModel Accessors
SVindex<- | KBModel Accessors
SVindex<--method | KBModel Accessors
SVMInformation | SVM Information Class
SVMInformation-class | SVM Information Class
svmModel | KBModel Accessors
svmModel-method | KBModel Accessors
svmModel<- | KBModel Accessors
svmModel<--method | KBModel Accessors
swdWeight | Position Dependent Kernel
SymmetricPairKernel | Symmetric Pair Kernel Class
symmetricPairKernel | Symmetric Pair Kernel
SymmetricPairKernel-class | Symmetric Pair Kernel Class

## -- T --

TFBS | KeBABS Sequence Data
tpr | ROCData Accessors
tpr-method | ROCData Accessors
tpr<- | ROCData Accessors
tpr<--method | ROCData Accessors
trainSVM | SVM Access for Training and Prediction
trainSVM-method | SVM Access for Training and Prediction

## -- W --

width | DNAVector, RNAVector, AAVector Objects and BioVector Class
width-method | DNAVector, RNAVector, AAVector Objects and BioVector Class

## -- Y --

yCC | KeBABS Sequence Data
yFB | KeBABS Sequence Data
yMC | KeBABS Sequence Data
yReg | KeBABS Sequence Data

## -- misc --

%*%-method | ExplicitRepresentation Accessors
[-method | DNAVector, RNAVector, AAVector Objects and BioVector Class
[-method | ExplicitRepresentation Accessors
[-method | KernelMatrix Accessors
[-method | PredictionProfile Accessors