HmmSnpCallSet-class {VanillaICE} | R Documentation

## Class HmmSnpCallSet

### Description

### Objects from the Class

Objects can be created by calls of the form `new("HmmSnpCallSet", assayData, phenoData, featureData, experimentData, annotation, chromosomeAnnotation, calls, callsConfidence, copyNumber, cnConfidence, ...)`.

### Slots

`probabilityCalledHomIfNormal`:
  Object of class `"numeric"`
`probabilityCalledHetIfLoh`:
  Object of class `"numeric"`
`predictions`:
  Object of class `"matrix"`
`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"`
`callsIce`:
  Object of class `"logical"`
`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 `hSet-class`, directly. Class `oligoSnpSet-class`, by class "hSet", distance 2. Class `SnpCallSet-class`, by class "hSet", distance 3. Class `SnpCopyNumberSet-class`, by class "hSet", distance 3, with explicit coerce. Class `SnpCallSet-class`, by class "hSet", distance 4. Class `class.eSet`, by class "hSet", distance 5. Class `VersionedBiobase-class`, by class "hSet", distance 6. Class `Versioned-class`, by class "hSet", distance 7. Class `SnpCopyNumberSet-class`, by class "hSet", distance 4, with explicit coerce. Class `class.eSet`, by class "hSet", distance 5, with explicit coerce. Class `VersionedBiobase-class`, by class "hSet", distance 6, with explicit coerce. Class `Versioned-class`, by class "hSet", distance 7, with explicit coerce.

### Methods

[
  `signature(x = "HmmSnpCallSet")`
calculateEmissionProbability
  `signature(object = "HmmSnpCallSet")`
callsIce
  `signature(object = "HmmSnpCallSet")`
coerce
  `signature(from = "AnnotatedSnpSet", to = "HmmSnpCallSet")`
getLohProbability
  `signature(object = "HmmSnpCallSet")`
getTransitionProbability
  `signature(object = "HmmSnpCallSet")`
hmm
  `signature(object = "HmmSnpCallSet")`
isMissing
  `signature(object = "HmmSnpCallSet")`
plotHmm
  `signature(object = "HmmSnpCallSet")`
predictions
  `signature(object = "HmmSnpCallSet")`
predictions<-
  `signature(object = "HmmSnpCallSet", value = "ANY")`
show
  `signature(object = "HmmSnpCallSet")`

### Note

### Author(s)

Robert Scharpf

### References

### See Also

`HmmSnpSet-class`, `HmmSnpCopyNumberSet-class`, `hSet-class`

### Examples

    showClass("HmmSnpCallSet")

[Package VanillaICE version 1.0.2 Index]