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 |
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 |
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 |
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 |
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 |