| 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<-,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<-,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" |
| 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 |