Entry: HmmOptions-class
Aliases: [,HmmOptions-method annotation,HmmOptions-method annotation<-,HmmOptions,ANY-method db,HmmOptions-method hmm,HmmOptions,HmmParameter-method initialize,HmmOptions-method notes,HmmOptions-method show,HmmOptions-method calculateDistance,HmmOptions-method physicalDistance,HmmOptions-method calls.ICE,HmmOptions-method calls.ICE<-,HmmOptions,logical-method copyNumber.ICE,HmmOptions-method copyNumber.ICE<-,HmmOptions,logical-method copyNumber.location,HmmOptions-method copyNumber.location,HmmOptions,numeric-method probHomCall,HmmOptions-method probHomCall<-,HmmOptions,numeric-method snpset,HmmOptions-method snpset<-,HmmOptions,SnpLevelSet-method states,HmmOptions-method states<-,HmmOptions,character-method term5,HmmOptions-method term5<-,HmmOptions,numeric-method HmmOptions-class
Keywords: classes
Description: Class "HmmOptions"
URL: ../../../library/VanillaICE/html/HmmOptions-class.html

Entry: HmmOptions-methods
Aliases: HmmOptions-methods copyNumber.location copyNumber.location<- probHomCall probHomCall<- snpset snpset<- term5 term5<-
Keywords: methods
Description: Accessors and replacement methods for HmmOptions
URL: ../../../library/VanillaICE/html/HmmOptions-methods.html

Entry: HmmParameter-class
Aliases: HmmParameter-class [,HmmParameter-method emission,HmmParameter-method emission<-,HmmParameter,array-method genomicDistance,HmmParameter-method genomicDistance<-,HmmParameter,numeric-method initialize,HmmParameter-method Pi,HmmParameter-method show,HmmParameter-method states,HmmParameter-method states<-,HmmParameter,character-method tau,HmmParameter-method transitionScale,HmmParameter-method transitionScale<-,HmmParameter,matrix-method
Keywords: classes
Description: Class "HmmParameter"
URL: ../../../library/VanillaICE/html/HmmParameter-class.html

Entry: HmmPredict-class
Aliases: HmmPredict-class SnpClass,HmmPredict-method [,HmmPredict-method breakpoints breakpoints,HmmPredict-method breakpoints<- breakpoints<-,HmmPredict-method breakpoints<-,HmmPredict,ANY-method calculateBreakpoints,HmmPredict-method chromosome,chromosome-method chromosome,HmmPredict-method fData,HmmPredict-method featureData,HmmPredict-method featureNames,HmmPredict-method getPar,HmmPredict-method initialize,HmmPredict-method position,HmmPredict-method predictions predictions<- predictions,HmmPredict-method predictions<-,HmmPredict,matrix-method sampleNames,HmmPredict-method show,HmmPredict-method states,HmmPredict-method summary,HmmPredict-method
Keywords: classes
Description: Class for the hidden Markov model results
URL: ../../../library/VanillaICE/html/HmmPredict-class.html

Entry: addFeatureData
Aliases: addFeatureData
Keywords: manip
Description: Adds chromosomal arm annotation to the featureData
URL: ../../../library/VanillaICE/html/addFeatureData.html

Entry: calculateBreakpoints
Aliases: calculateBreakpoints
Keywords: manip methods
Description: Calculate breakpoints for altered states from the prediction matrix
URL: ../../../library/VanillaICE/html/calculateBreakpoints.html

Entry: calculateCnSE
Aliases: calculateCnSE
Keywords: manip
Description: Calculates copy number standard errors
URL: ../../../library/VanillaICE/html/calculateCnSE.html

Entry: calculateDistance
Aliases: calculateDistance physicalDistance calculateDistance,SnpLevelSet-method physicalDistance,SnpLevelSet-method
Keywords: methods manip
Description: Calculates the physical distance between adjacent SNPs
URL: ../../../library/VanillaICE/html/calculateDistance.html

Entry: calls.ICE
Aliases: calls.ICE calls.ICE<-
Keywords: methods
Description: Indicates whether to use confidence scores of the observed copy number estimates in the HMM
URL: ../../../library/VanillaICE/html/calls.ICE.html

Entry: calls.emission
Aliases: calls.emission
Keywords: methods
Description: Calculates emission probabilities for the genotype calls
URL: ../../../library/VanillaICE/html/calls.emission.html

Entry: chromosome1
Aliases: chromosome1
Keywords: datasets
Description: Simulated chromosome 1
URL: ../../../library/VanillaICE/html/chromosome1.html

Entry: copyNumber.ICE
Aliases: copyNumber.ICE copyNumber.ICE<-
Keywords: methods
Description: Indicates whether to use confidence scores of the observed copy number estimates in the HMM
URL: ../../../library/VanillaICE/html/copyNumber.ICE.html

Entry: copyNumber.emission
Aliases: copyNumber.emission
Keywords: methods
Description: Calculate emission probabilities for copy number
URL: ../../../library/VanillaICE/html/copyNumber.emission.html

Entry: copynumberEmission
Aliases: copynumberEmission
Keywords: methods
Description: Emission probabilities for copy number
URL: ../../../library/VanillaICE/html/copynumberEmission.html

Entry: emission
Aliases: emission emission<-
Keywords: methods
Description: Accessor for emission probabilities
URL: ../../../library/VanillaICE/html/emission.html

Entry: findBreaks
Aliases: findBreaks
Keywords: manip
Description: Identify breakpoints from the hidden Markov model predictions
URL: ../../../library/VanillaICE/html/findBreaks.html

Entry: fit
Aliases: fit
Keywords: datasets
Description: Object of class HmmPredict
URL: ../../../library/VanillaICE/html/fit.html

Entry: genomicDistance
Aliases: genomicDistance tau genomicDistance<-
Keywords: methods
Description: A rough estimate of the genomic distance between SNPs
URL: ../../../library/VanillaICE/html/genomicDistance.html

Entry: genotypeEmission
Aliases: genotypeEmission
Keywords: methods
Description: Emission probabilities for di-allelic genotype calls
URL: ../../../library/VanillaICE/html/genotypeEmission.html

Entry: getChromosomeArm
Aliases: getChromosomeArm
Keywords: manip
Description: Get the chromosome arm
URL: ../../../library/VanillaICE/html/getChromosomeArm.html

Entry: hmm
Aliases: hmm
Keywords: models
Description: Fits the hidden Markov model
URL: ../../../library/VanillaICE/html/hmm.html

Entry: Pi
Aliases: Pi
Keywords: methods
Description: Accessor for the initial state probabilities of the hidden Markov model
URL: ../../../library/VanillaICE/html/pi.html

Entry: scaleTransitionProbability
Aliases: scaleTransitionProbability
Keywords: manip
Description: Scales the probability of transitioning between two states in the Viterbi algorithm
URL: ../../../library/VanillaICE/html/scaleTransitionProbability.html

Entry: states
Aliases: states states<-
Keywords: methods
Description: Accessor and replacement method for the hidden states of the Markov model
URL: ../../../library/VanillaICE/html/states.html

Entry: transitionScale
Aliases: transitionScale transitionScale<-
Keywords: methods
Description: Scales the transition probabilities of the hidden Markov model
URL: ../../../library/VanillaICE/html/transitionScale.html

Entry: viterbi
Aliases: viterbi
Keywords: models
Description: viterbi algorithm
URL: ../../../library/VanillaICE/html/viterbi.html
