| 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 |