Kernel-Based Analysis Of Biological Sequences


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Documentation for package ‘kebabs’ version 1.30.0

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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

-- misc --

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