Methods for fitting Hidden Markov Models to SNP chip data


[Package List] [Top]

Documentation for package ‘VanillaICE’ version 1.0.2

User Guides and Package Vignettes

Read overview or browse directory.

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