hSet-class {VanillaICE} | R Documentation

## Virtual class for fitting HMMs to SNP chip data

### Description

### Objects from the Class

A virtual Class: No objects may be created from it.

### Slots

`distance`:
  Object of class `"logical"`
`initialStateProbability`:
  Object of class `"NullOrNumeric"`
`transitionProbability`:
  Object of class `"NullOrNumericOrMatrix"`
`emissionProbability`:
  Object of class `"NullOrMatrix"`
`likelihood`:
  Object of class `"NullOrMatrix"`
`chromosomeArm`:
  Object of class `"character"`
`stateNames`:
  Object of class `"character"`
`chromosomeAnnotation`:
  Object of class `"data.frame"`
`assayData`:
  Object of class `"AssayData"`
`phenoData`:
  Object of class `"AnnotatedDataFrame"`
`featureData`:
  Object of class `"AnnotatedDataFrame"`
`experimentData`:
  Object of class `"MIAME"`
`annotation`:
  Object of class `"character"`
`.__classVersion__`:
  Object of class `"Versions"`

### Extends

Class `AnnotatedSnpSet-class`, directly. Class `AnnotatedSnpCallSet-class`, by class "AnnotatedSnpSet", distance 2. Class `AnnotatedSnpCopyNumberSet-class`, by class "AnnotatedSnpSet", distance 2, with explicit coerce. Class `SnpCallSet-clas`, by class "AnnotatedSnpSet", distance 3. Class `class.eSet`, by class "AnnotatedSnpSet", distance 4. Class `VersionedBiobase-class`, by class "AnnotatedSnpSet", distance 5. Class `Versioned-class`, by class "AnnotatedSnpSet", distance 6. Class `SnpCopyNumberSet-class`, by class "AnnotatedSnpSet", distance 3, with explicit coerce. Class `class.eSet`, by class "AnnotatedSnpSet", distance 4, with explicit coerce. Class `VersionedBiobase-class`, by class "AnnotatedSnpSet", distance 5, with explicit coerce. Class `Versioned-class`, by class "AnnotatedSnpSet", distance 6, with explicit coerce.

### Methods

chromosomeArm
  `signature(object = "hSet")`
chromosomeArm<-
  `signature(object = "hSet")`
distance
  `signature(object = "hSet")`
distance<-
  `signature(object = "hSet")`
emissionProbability
  `signature(object = "hSet")`
emissionProbability<-
  `signature(object = "hSet")`
hmmBySample
  `signature(object = "hSet")`
initialStateProbability
  `signature(object = "hSet")`
initialStateProbability<-
  `signature(object = "hSet")`
likelihood
  `signature(object = "hSet")`
likelihood<-
  `signature(object = "hSet")`
numberStates
  `signature(object = "hSet")`
stateNames
  `signature(object = "hSet")`
stateNames<-
  `signature(object = "hSet")`
transitionProbability
  `signature(object = "hSet")`
transitionProbability<-
  `signature(object = "hSet")`
viterbi
  `signature(object = "hSet")`

### Note

### Author(s)

### References

Robert Scharpf

### See Also

`HmmSnpSet-class`, `HmmSnpCopyNumberSet-class`, `HmmSnpCallSet-class`

### Examples

    showClass("hSet")

[Package VanillaICE version 1.0.2 Index]