Kernel-Based Analysis of Biological Sequences

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Documentation for package ‘kebabs’ version 1.38.0

• 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