Methods for fitting Hidden Markov Models to SNP chip data


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Documentation for package ‘VanillaICE’ version 1.4.0

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A B C D E F G H I N P S T V misc

-- A --

addFeatureData Adds chromosomal arm annotation to the featureData
annotation,HmmOptions-method Class "HmmOptions"
annotation<-,HmmOptions,ANY-method Class "HmmOptions"

-- B --

breakpoints Class for the hidden Markov model results
breakpoints,HmmPredict-method Class for the hidden Markov model results
breakpoints<-,HmmPredict,ANY-method Class for the hidden Markov model results
breakpoints<-,HmmPredict-method Class for the hidden Markov model results

-- C --

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

-- D --

db,HmmOptions-method Class "HmmOptions"

-- E --

emission Accessor for emission probabilities
emission,HmmParameter-method Class "HmmParameter"
emission<-,HmmParameter,array-method Class "HmmParameter"

-- F --

fData,HmmPredict-method Class for the hidden Markov model results
featureData,HmmPredict-method Class for the hidden Markov model results
featureNames,HmmPredict-method Class for the hidden Markov model results
findBreaks Identify breakpoints from the hidden Markov model predictions
fit Object of class HmmPredict

-- G --

genomicDistance A rough estimate of the genomic distance between SNPs
genomicDistance,HmmParameter-method Class "HmmParameter"
genomicDistance<-,HmmParameter,numeric-method Class "HmmParameter"
genotypeEmission Emission probabilities for di-allelic genotype calls
getChromosomeArm Get the chromosome arm
getPar,HmmPredict-method Class for the hidden Markov model results

-- H --

hmm Fits the hidden Markov model
hmm,HmmOptions,HmmParameter-method Class "HmmOptions"
HmmOptions-class Class "HmmOptions"
HmmOptions-methods Accessors and replacement methods for HmmOptions
HmmParameter-class Class "HmmParameter"
HmmPredict-class Class for the hidden Markov model results

-- I --

initialize,HmmOptions-method Class "HmmOptions"
initialize,HmmParameter-method Class "HmmParameter"
initialize,HmmPredict-method Class for the hidden Markov model results

-- N --

notes,HmmOptions-method Class "HmmOptions"

-- P --

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"

-- S --

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

-- T --

tau A rough estimate of the genomic distance between SNPs
tau,HmmParameter-method Class "HmmParameter"
term5 Accessors and replacement methods for HmmOptions
term5,HmmOptions-method Class "HmmOptions"
term5<-,HmmOptions,numeric-method Class "HmmOptions"
transitionScale Scales the transition probabilities of the hidden Markov model
transitionScale,HmmParameter-method Class "HmmParameter"
transitionScale<-,HmmParameter,matrix-method Class "HmmParameter"

-- V --

viterbi viterbi algorithm

-- misc --

[,HmmOptions-method Class "HmmOptions"
[,HmmParameter-method Class "HmmParameter"
[,HmmPredict-method Class for the hidden Markov model results