Entry: HmmSnpCallSet-class
Aliases: HmmSnpCallSet-class [,HmmSnpCallSet-method bind,HmmSnpCallSet,HmmSnpCallSet-method bind,NULL,HmmSnpCallSet-method bind,HmmSnpCallSet,NULL-method calculateEmissionProbability,HmmSnpCallSet-method callsIce,HmmSnpCallSet-method callsIce<-,HmmSnpCallSet,logical-method coerce,oligoSnpSet,HmmSnpCallSet-method coerce,HmmSnpSet,HmmSnpCallSet-method coerce,SnpCallSet,HmmSnpCallSet-method getInitialStateProbability,HmmSnpCallSet-method getLohProbability,HmmSnpCallSet-method getTransitionProbability,HmmSnpCallSet-method hmm,HmmSnpCallSet-method initialize,HmmSnpCallSet-method isMissing,HmmSnpCallSet-method pCHOM,HmmSnpCallSet-method pCHOM<-,HmmSnpCallSet-method show,HmmSnpCallSet-method
Keywords: classes
Description: Class HmmSnpCallSet
URL: ../../../library/VanillaICE/html/HmmSnpCallSet-class.html

Entry: HmmSnpCopyNumberSet-class
Aliases: HmmSnpCopyNumberSet-class [,HmmSnpCopyNumberSet-method bind,HmmSnpCopyNumberSet,HmmSnpCopyNumberSet-method bind,NULL,HmmSnpCopyNumberSet-method bind,HmmSnpCopyNumberSet,NULL-method calculateEmissionProbability,HmmSnpCopyNumberSet-method coerce,oligoSnpSet,HmmSnpCopyNumberSet-method coerce,HmmSnpSet,HmmSnpCopyNumberSet-method coerce,SnpCopyNumberSet,HmmSnpCopyNumberSet-method copyNumberIce,HmmSnpCopyNumberSet-method copyNumberIce<-,HmmSnpCopyNumberSet,logical-method getCopyNumberLocation,HmmSnpCopyNumberSet-method getCopyNumberScale,HmmSnpCopyNumberSet-method getInitialStateProbability,HmmSnpCopyNumberSet-method getTransitionProbability,HmmSnpCopyNumberSet-method hmm,HmmSnpCopyNumberSet-method initialize,HmmSnpCopyNumberSet-method locationCopyNumber,HmmSnpCopyNumberSet-method locationCopyNumber<-,HmmSnpCopyNumberSet-method scaleCopyNumber,HmmSnpCopyNumberSet-method scaleCopyNumber<-,HmmSnpCopyNumberSet-method show,HmmSnpCopyNumberSet-method
Keywords: classes
Description: HmmSnpCopyNumberSet
URL: ../../../library/VanillaICE/html/HmmSnpCopyNumberSet-class.html

Entry: HmmSnpSet-class
Aliases: HmmSnpSet-class [,HmmSnpSet-method [<-,HmmSnpSet-method bind,HmmSnpSet,HmmSnpSet-method bind,NULL,HmmSnpSet-method bind,HmmSnpSet,NULL-method breakpoints,HmmSnpSet-method calculateEmissionProbability,HmmSnpSet-method coerce,oligoSnpSet,HmmSnpSet-method getCopyNumberLocation,HmmSnpSet-method getCopyNumberScale,HmmSnpSet-method getInitialStateProbability,HmmSnpSet-method getLohProbability,HmmSnpSet-method getTransitionProbability,HmmSnpSet-method hmm,HmmSnpSet-method ice2VanillaICE ice2VanillaICE,HmmSnpSet-method initialize,HmmSnpSet-method locationCopyNumber,HmmSnpSet-method locationCopyNumber<-,HmmSnpSet-method pCHOM,HmmSnpSet-method pCHOM<-,HmmSnpSet-method predictions,HmmSnpSet-method predictions<-,HmmSnpSet,matrix-method scaleCopyNumber,HmmSnpSet-method scaleCopyNumber<-,HmmSnpSet-method show,HmmSnpSet-method .unsplitHmm .unsplitHmm,list,AnnotatedDataFrame-method
Keywords: classes
Description: HmmSnpSet
URL: ../../../library/VanillaICE/html/HmmSnpSet-class.html

Entry: ParHSet-class
Aliases: ParHSet-class initialize,ParHSet-method plotSnp,ParHSet,ANY-method
Keywords: classes
Description: Class ParHSet
URL: ../../../library/VanillaICE/html/ParHSet-class.html

Entry: ParHmmSnpCallSet-class
Aliases: ParHmmSnpCallSet-class initialize,ParHmmSnpCallSet-method plotSnp,ParHmmSnpCallSet,HmmSnpCallSet-method
Keywords: classes
Description: Class ParHmmSnpCallSet
URL: ../../../library/VanillaICE/html/ParHmmSnpCallSet-class.html

Entry: ParHmmSnpCopyNumberSet-class
Aliases: ParHmmSnpCopyNumberSet-class initialize,ParHmmSnpCopyNumberSet-method plotSnp,ParHmmSnpCopyNumberSet,HmmSnpCopyNumberSet-method
Keywords: classes
Description: Class ParHmmSnpCopyNumberSet
URL: ../../../library/VanillaICE/html/ParHmmSnpCopyNumberSet-class.html

Entry: ParHmmSnpSet-class
Aliases: ParHmmSnpSet-class initialize,ParHmmSnpSet-method plotSnp,ParHmmSnpSet,HmmSnpSet-method
Keywords: classes
Description: Graphical parameters
URL: ../../../library/VanillaICE/html/ParHmmSnpSet-class.html

Entry: bind
Aliases: bind
Keywords: methods
Description: Combine two objects of the same class
URL: ../../../library/VanillaICE/html/bind.html

Entry: breakpoints
Aliases: breakpoints
Keywords: manip attribute
Description: Locations of breakpoints from the HMM
URL: ../../../library/VanillaICE/html/breakpoints.html

Entry: byArm
Aliases: byArm
Keywords: methods
Description: Fits the HMM to each chromosomal arm
URL: ../../../library/VanillaICE/html/byArm.html

Entry: calculateEmissionProbability
Aliases: calculateEmissionProbability
Keywords: methods
Description: Calculates emission probabilities for the HMM
URL: ../../../library/VanillaICE/html/calculateEmissionProbability.html

Entry: callEmission
Aliases: callEmission
Keywords: manip
Description: Calculate emission probabilities for the ICE HMM
URL: ../../../library/VanillaICE/html/callEmission.html

Entry: callsIce
Aliases: callsIce callsIce<-
Keywords: methods
Description: Indicates whether to use confidence estimates of the genotype calls in the HMM
URL: ../../../library/VanillaICE/html/callsIce.html

Entry: chromosome1
Aliases: chromosome1
Keywords: datasets
Description: Simulated chromosome 1
URL: ../../../library/VanillaICE/html/chromosome1.html

Entry: chromosomeArm
Aliases: chromosomeArm chromosomeArm<-
Keywords: methods
Description: Accessor for chromosome arm
URL: ../../../library/VanillaICE/html/chromosomeArm.html

Entry: copyNumberIce
Aliases: copyNumberIce copyNumberIce<-
Keywords: methods
Description: Whether to use the uncertainty estimates of the copy number in the HMM
URL: ../../../library/VanillaICE/html/copyNumberIce.html

Entry: distance
Aliases: distance distance<-
Keywords: methods
Description: Accessor for distance
URL: ../../../library/VanillaICE/html/distance.html

Entry: emissionProbability
Aliases: emissionProbability emissionProbability<-
Keywords: methods
Description: Accessor for the emission probabilities
URL: ../../../library/VanillaICE/html/emissionProbability.html

Entry: getCallEmission
Aliases: getCallEmission
Keywords: manip
Description: Calculates emission probabilities for genotype calls
URL: ../../../library/VanillaICE/html/getCallEmission.html

Entry: getCopyNumberLocation
Aliases: getCopyNumberLocation
Keywords: attribute
Description: Typically the mean copy number for the hidden states
URL: ../../../library/VanillaICE/html/getCopyNumberLocation.html

Entry: getCopyNumberScale
Aliases: getCopyNumberScale
Keywords: attribute
Description: Scale parameter used for Gaussian distribution of copy number
URL: ../../../library/VanillaICE/html/getCopyNumberScale.html

Entry: getHapmapProbabilities
Aliases: getHapmapProbabilities
Keywords: nonparametric
Description: Estimate probability of correct genotype call
URL: ../../../library/VanillaICE/html/getHapmapProbabilities.html

Entry: getInitialStateProbability
Aliases: getInitialStateProbability
Keywords: attribute
Description: Initial state probabilities
URL: ../../../library/VanillaICE/html/getInitialStateProbability.html

Entry: getLohProbability
Aliases: getLohProbability
Keywords: attribute
Description: Emission probabilities for LOH
URL: ../../../library/VanillaICE/html/getLohProbability.html

Entry: getTransitionProbability
Aliases: getTransitionProbability
Keywords: attribute
Description: Transition probabilities for the HMM
URL: ../../../library/VanillaICE/html/getTransitionProbability.html

Entry: hSet-class
Aliases: hSet-class breakpoints,hSet-method byArm,hSet-method callsIce,hSet-method callsIce<-,hSet,logical-method copyNumberIce,hSet-method copyNumberIce<-,hSet,logical-method chromosomeArm,hSet-method chromosomeArm<-,hSet-method distance,hSet-method distance<-,hSet-method emissionProbability,hSet-method emissionProbability<-,hSet-method getBreaks getBreaks,hSet-method getPar,hSet-method hmmBySample,hSet-method initialStateProbability,hSet-method initialStateProbability<-,hSet-method isMissing,hSet-method likelihood,hSet-method likelihood<-,hSet-method numberStates,hSet-method plotSnp,hSet-method predictions,hSet-method predictions<-,hSet,ANY-method stateNames,hSet-method stateNames<-,hSet-method transitionProbability,hSet-method transitionProbability<-,hSet-method viterbi,hSet-method
Keywords: classes
Description: Virtual class for fitting HMMs to SNP chip data
URL: ../../../library/VanillaICE/html/hSet-class.html

Entry: hapmapProbabilities
Aliases: hapmapProbabilities
Keywords: data
Description: CRLMM confidence scores on HapMap data
URL: ../../../library/VanillaICE/html/hapmapProbabilities.html

Entry: hmm
Aliases: hmm
Keywords: models smooth
Description: Fits hidden Markov models to high throughput SNP chip data.
URL: ../../../library/VanillaICE/html/hmm.html

Entry: hmmBySample
Aliases: hmmBySample
Keywords: methods
Description: Fits HMM to a single sample
URL: ../../../library/VanillaICE/html/hmmBySample.html

Entry: initialStateProbability
Aliases: initialStateProbability initialStateProbability<-
Keywords: attribute methods
Description: Retrieves initial state probabilities
URL: ../../../library/VanillaICE/html/initialStateProbability.html

Entry: isMissing
Aliases: isMissing
Keywords: methods
Description: Checks for missing genotype calls
URL: ../../../library/VanillaICE/html/isMissing.html

Entry: likelihood
Aliases: likelihood likelihood<-
Keywords: methods
Description: The partial likelihood
URL: ../../../library/VanillaICE/html/likelihood.html

Entry: locationCopyNumber
Aliases: locationCopyNumber locationCopyNumber<-
Keywords: methods
Description: Location parameters for the copy number distribution (Gaussian)
URL: ../../../library/VanillaICE/html/locationCopyNumber.html

Entry: numberStates
Aliases: numberStates numberStates<-
Keywords: methods
Description: Number of hidden states
URL: ../../../library/VanillaICE/html/numberStates.html

Entry: pCHOM
Aliases: pCHOM pCHOM<-
Keywords: methods
Description: Probability of a homozygous genotype calls
URL: ../../../library/VanillaICE/html/pCHOM.html

Entry: plotPredictions
Aliases: plotPredictions
Keywords: aplot
Description: Plots the predicted states versus physical position
URL: ../../../library/VanillaICE/html/plotPredictions.html

Entry: predictions
Aliases: predictions predictions<-
Keywords: methods
Description: Predicted states from the HMM
URL: ../../../library/VanillaICE/html/predictions.html

Entry: scaleCopyNumber
Aliases: scaleCopyNumber scaleCopyNumber<-
Keywords: methods
Description: Variance parameters for the copy number distribution (Gaussian)
URL: ../../../library/VanillaICE/html/scaleCopyNumber.html

Entry: stateNames
Aliases: stateNames stateNames<-
Keywords: methods
Description: The hidden states
URL: ../../../library/VanillaICE/html/stateNames.html

Entry: transitionProbability
Aliases: transitionProbability transitionProbability<-
Keywords: methods
Description: Transition probabilities in the HMM
URL: ../../../library/VanillaICE/html/transitionProbability.html

Entry: viterbi
Aliases: viterbi
Keywords: methods
Description: viterbi algorithm
URL: ../../../library/VanillaICE/html/viterbi.html
