# Methods for fitting Hidden Markov Models to SNP chip data

## Documentation for package ‘VanillaICE’ version 1.0.2

## User Guides and Package Vignettes

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## Help Pages

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

.unsplitHmm | HmmSnpSet
.unsplitHmm,list,AnnotatedDataFrame-method | HmmSnpSet

## -- B --

bind | Combine two objects of the same class
bind,HmmSnpCallSet,HmmSnpCallSet-method | Class HmmSnpCallSet
bind,HmmSnpCallSet,NULL-method | Class HmmSnpCallSet
bind,HmmSnpCopyNumberSet,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
bind,HmmSnpCopyNumberSet,NULL-method | HmmSnpCopyNumberSet
bind,HmmSnpSet,HmmSnpSet-method | HmmSnpSet
bind,HmmSnpSet,NULL-method | HmmSnpSet
bind,NULL,HmmSnpCallSet-method | Class HmmSnpCallSet
bind,NULL,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
bind,NULL,HmmSnpSet-method | HmmSnpSet
breakpoints | Locations of breakpoints from the HMM
breakpoints,HmmSnpSet-method | HmmSnpSet
breakpoints,hSet-method | Virtual class for fitting HMMs to SNP chip data
byArm | Fits the HMM to each chromosomal arm
byArm,hSet-method | Virtual class for fitting HMMs to SNP chip data

## -- C --

calculateEmissionProbability | Calculates emission probabilities for the HMM
calculateEmissionProbability,HmmSnpCallSet-method | Class HmmSnpCallSet
calculateEmissionProbability,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
calculateEmissionProbability,HmmSnpSet-method | HmmSnpSet
callEmission | Calculate emission probabilities for the ICE HMM
callsIce | Indicates whether to use confidence estimates of the genotype calls in the HMM
callsIce,HmmSnpCallSet-method | Class HmmSnpCallSet
callsIce,hSet-method | Virtual class for fitting HMMs to SNP chip data
callsIce<-,HmmSnpCallSet,logical-method | Class HmmSnpCallSet
callsIce<-,hSet,logical-method | Virtual class for fitting HMMs to SNP chip data
chromosome1 | Simulated chromosome 1
chromosomeArm | Accessor for chromosome arm
chromosomeArm,hSet-method | Virtual class for fitting HMMs to SNP chip data
chromosomeArm<-,hSet-method | Virtual class for fitting HMMs to SNP chip data
coerce,HmmSnpSet,HmmSnpCallSet-method | Class HmmSnpCallSet
coerce,HmmSnpSet,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
coerce,oligoSnpSet,HmmSnpCallSet-method | Class HmmSnpCallSet
coerce,oligoSnpSet,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
coerce,oligoSnpSet,HmmSnpSet-method | HmmSnpSet
coerce,SnpCallSet,HmmSnpCallSet-method | Class HmmSnpCallSet
coerce,SnpCopyNumberSet,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
copyNumberIce | Whether to use the uncertainty estimates of the copy number in the HMM
copyNumberIce,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
copyNumberIce,hSet-method | Virtual class for fitting HMMs to SNP chip data
copyNumberIce<-,HmmSnpCopyNumberSet,logical-method | HmmSnpCopyNumberSet
copyNumberIce<-,hSet,logical-method | Virtual class for fitting HMMs to SNP chip data

## -- D --

distance | Accessor for distance
distance,hSet-method | Virtual class for fitting HMMs to SNP chip data
distance<-,hSet-method | Virtual class for fitting HMMs to SNP chip data

## -- E --

emissionProbability | Accessor for the emission probabilities
emissionProbability,hSet-method | Virtual class for fitting HMMs to SNP chip data
emissionProbability<-,hSet-method | Virtual class for fitting HMMs to SNP chip data

## -- G --

getBreaks | Virtual class for fitting HMMs to SNP chip data
getBreaks,hSet-method | Virtual class for fitting HMMs to SNP chip data
getCallEmission | Calculates emission probabilities for genotype calls
getCopyNumberLocation | Typically the mean copy number for the hidden states
getCopyNumberLocation,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
getCopyNumberLocation,HmmSnpSet-method | HmmSnpSet
getCopyNumberScale | Scale parameter used for Gaussian distribution of copy number
getCopyNumberScale,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
getCopyNumberScale,HmmSnpSet-method | HmmSnpSet
getHapmapProbabilities | Estimate probability of correct genotype call
getInitialStateProbability | Initial state probabilities
getInitialStateProbability,HmmSnpCallSet-method | Class HmmSnpCallSet
getInitialStateProbability,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
getInitialStateProbability,HmmSnpSet-method | HmmSnpSet
getLohProbability | Emission probabilities for LOH
getLohProbability,HmmSnpCallSet-method | Class HmmSnpCallSet
getLohProbability,HmmSnpSet-method | HmmSnpSet
getPar,hSet-method | Virtual class for fitting HMMs to SNP chip data
getTransitionProbability | Transition probabilities for the HMM
getTransitionProbability,HmmSnpCallSet-method | Class HmmSnpCallSet
getTransitionProbability,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
getTransitionProbability,HmmSnpSet-method | HmmSnpSet

## -- H --

hapmapProbabilities | CRLMM confidence scores on HapMap data
hmm | Fits hidden Markov models to high throughput SNP chip data.
hmm,HmmSnpCallSet-method | Class HmmSnpCallSet
hmm,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
hmm,HmmSnpSet-method | HmmSnpSet
hmmBySample | Fits HMM to a single sample
hmmBySample,hSet-method | Virtual class for fitting HMMs to SNP chip data
HmmSnpCallSet-class | Class HmmSnpCallSet
HmmSnpCopyNumberSet-class | HmmSnpCopyNumberSet
HmmSnpSet-class | HmmSnpSet
hSet-class | Virtual class for fitting HMMs to SNP chip data

## -- I --

ice2VanillaICE | HmmSnpSet
ice2VanillaICE,HmmSnpSet-method | HmmSnpSet
initialize,HmmSnpCallSet-method | Class HmmSnpCallSet
initialize,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
initialize,HmmSnpSet-method | HmmSnpSet
initialize,ParHmmSnpCallSet-method | Class ParHmmSnpCallSet
initialize,ParHmmSnpCopyNumberSet-method | Class ParHmmSnpCopyNumberSet
initialize,ParHmmSnpSet-method | Graphical parameters
initialize,ParHSet-method | Class ParHSet
initialStateProbability | Retrieves initial state probabilities
initialStateProbability,hSet-method | Virtual class for fitting HMMs to SNP chip data
initialStateProbability<-,hSet-method | Virtual class for fitting HMMs to SNP chip data
isMissing | Checks for missing genotype calls
isMissing,HmmSnpCallSet-method | Class HmmSnpCallSet
isMissing,hSet-method | Virtual class for fitting HMMs to SNP chip data

## -- L --

likelihood | The partial likelihood
likelihood,hSet-method | Virtual class for fitting HMMs to SNP chip data
likelihood<-,hSet-method | Virtual class for fitting HMMs to SNP chip data
locationCopyNumber | Location parameters for the copy number distribution (Gaussian)
locationCopyNumber,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
locationCopyNumber,HmmSnpSet-method | HmmSnpSet
locationCopyNumber<-,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
locationCopyNumber<-,HmmSnpSet-method | HmmSnpSet

## -- N --

numberStates | Number of hidden states
numberStates,hSet-method | Virtual class for fitting HMMs to SNP chip data

## -- P --

ParHmmSnpCallSet-class | Class ParHmmSnpCallSet
ParHmmSnpCopyNumberSet-class | Class ParHmmSnpCopyNumberSet
ParHmmSnpSet-class | Graphical parameters
ParHSet-class | Class ParHSet
pCHOM | Probability of a homozygous genotype calls
pCHOM,HmmSnpCallSet-method | Class HmmSnpCallSet
pCHOM,HmmSnpSet-method | HmmSnpSet
pCHOM<-,HmmSnpCallSet-method | Class HmmSnpCallSet
pCHOM<-,HmmSnpSet-method | HmmSnpSet
plotPredictions | Plots the predicted states versus physical position
plotSnp,hSet-method | Virtual class for fitting HMMs to SNP chip data
plotSnp,ParHmmSnpCallSet,HmmSnpCallSet-method | Class ParHmmSnpCallSet
plotSnp,ParHmmSnpCopyNumberSet,HmmSnpCopyNumberSet-method | Class ParHmmSnpCopyNumberSet
plotSnp,ParHmmSnpSet,HmmSnpSet-method | Graphical parameters
plotSnp,ParHSet,ANY-method | Class ParHSet
predictions | Predicted states from the HMM
predictions,HmmSnpSet-method | HmmSnpSet
predictions,hSet-method | Virtual class for fitting HMMs to SNP chip data
predictions<-,HmmSnpSet,matrix-method | HmmSnpSet
predictions<-,hSet,ANY-method | Virtual class for fitting HMMs to SNP chip data

## -- S --

scaleCopyNumber | Variance parameters for the copy number distribution (Gaussian)
scaleCopyNumber,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
scaleCopyNumber,HmmSnpSet-method | HmmSnpSet
scaleCopyNumber<-,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
scaleCopyNumber<-,HmmSnpSet-method | HmmSnpSet
show,HmmSnpCallSet-method | Class HmmSnpCallSet
show,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
show,HmmSnpSet-method | HmmSnpSet
stateNames | The hidden states
stateNames,hSet-method | Virtual class for fitting HMMs to SNP chip data
stateNames<-,hSet-method | Virtual class for fitting HMMs to SNP chip data

## -- T --

transitionProbability | Transition probabilities in the HMM
transitionProbability,hSet-method | Virtual class for fitting HMMs to SNP chip data
transitionProbability<-,hSet-method | Virtual class for fitting HMMs to SNP chip data

## -- V --

viterbi | viterbi algorithm
viterbi,hSet-method | Virtual class for fitting HMMs to SNP chip data

## -- misc --

[,HmmSnpCallSet-method | Class HmmSnpCallSet
[,HmmSnpCopyNumberSet-method | HmmSnpCopyNumberSet
[,HmmSnpSet-method | HmmSnpSet
[<-,HmmSnpSet-method | HmmSnpSet