calculateBreakpoints |
Calculate breakpoints for altered states from the prediction matrix |
calculateBreakpoints,HmmPredict-method |
Class for the hidden Markov model results |
calculateCnSE |
Calculates copy number standard errors |
calculateDistance |
Calculates the physical distance between adjacent SNPs |
calculateDistance,HmmOptions-method |
Class "HmmOptions" |
calculateDistance,SnpLevelSet-method |
Calculates the physical distance between adjacent SNPs |
calls.emission |
Calculates emission probabilities for the genotype calls |
calls.ICE |
Indicates whether to use confidence scores of the observed copy number estimates in the HMM |
calls.ICE,HmmOptions-method |
Class "HmmOptions" |
calls.ICE<- |
Indicates whether to use confidence scores of the observed copy number estimates in the HMM |
calls.ICE<-,HmmOptions,logical-method |
Class "HmmOptions" |
chromosome,chromosome-method |
Class for the hidden Markov model results |
chromosome,HmmPredict-method |
Class for the hidden Markov model results |
chromosome1 |
Simulated chromosome 1 |
copyNumber.emission |
Calculate emission probabilities for copy number |
copyNumber.ICE |
Indicates whether to use confidence scores of the observed copy number estimates in the HMM |
copyNumber.ICE,HmmOptions-method |
Class "HmmOptions" |
copyNumber.ICE<- |
Indicates whether to use confidence scores of the observed copy number estimates in the HMM |
copyNumber.ICE<-,HmmOptions,logical-method |
Class "HmmOptions" |
copyNumber.location |
Accessors and replacement methods for HmmOptions |
copyNumber.location,HmmOptions,numeric-method |
Class "HmmOptions" |
copyNumber.location,HmmOptions-method |
Class "HmmOptions" |
copyNumber.location<- |
Accessors and replacement methods for HmmOptions |
copynumberEmission |
Emission probabilities for copy number |
physicalDistance |
Calculates the physical distance between adjacent SNPs |
physicalDistance,HmmOptions-method |
Class "HmmOptions" |
physicalDistance,SnpLevelSet-method |
Calculates the physical distance between adjacent SNPs |
Pi |
Accessor for the initial state probabilities of the hidden Markov model |
Pi,HmmParameter-method |
Class "HmmParameter" |
position,HmmPredict-method |
Class for the hidden Markov model results |
predictions |
Class for the hidden Markov model results |
predictions,HmmPredict-method |
Class for the hidden Markov model results |
predictions<-,HmmPredict,matrix-method |
Class for the hidden Markov model results |
probHomCall |
Accessors and replacement methods for HmmOptions |
probHomCall,HmmOptions-method |
Class "HmmOptions" |
probHomCall<-,HmmOptions,numeric-method |
Class "HmmOptions" |
sampleNames,HmmPredict-method |
Class for the hidden Markov model results |
scaleTransitionProbability |
Scales the probability of transitioning between two states in the Viterbi algorithm |
show,HmmOptions-method |
Class "HmmOptions" |
show,HmmParameter-method |
Class "HmmParameter" |
show,HmmPredict-method |
Class for the hidden Markov model results |
SnpClass,HmmPredict-method |
Class for the hidden Markov model results |
snpset |
Accessors and replacement methods for HmmOptions |
snpset,HmmOptions-method |
Class "HmmOptions" |
snpset<-,HmmOptions,SnpLevelSet-method |
Class "HmmOptions" |
states |
Accessor and replacement method for the hidden states of the Markov model |
states,HmmOptions-method |
Class "HmmOptions" |
states,HmmParameter-method |
Class "HmmParameter" |
states,HmmPredict-method |
Class for the hidden Markov model results |
states<-,HmmOptions,character-method |
Class "HmmOptions" |
states<-,HmmParameter,character-method |
Class "HmmParameter" |
summary,HmmPredict-method |
Class for the hidden Markov model results |