# Methods for fitting Hidden Markov Models to SNP chip data

## Documentation for package ‘VanillaICE’ version 1.4.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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