HmmSnpSet-class {VanillaICE} | R Documentation

## HmmSnpSet

### Description

### Objects from the Class

Objects can be created by calls of the form `new("HmmSnpSet", assayData, featureData, phenoData, experimentData, annotation, calls, callsConfidence, copyNumber, cnConfidence, predictions, scaleCopyNumber, probabilityCalledHomIfNormal, probabilityCalledHetIfLoh, log2, locationCopyNumber, stateNames, ...)`.

### Slots

`locationCopyNumber`:
  Object of class `"numeric"`
`scaleCopyNumber`:
  Object of class `"NullOrMatrix"`
`log2`:
  Object of class `"logical"`
`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"`
`copyNumberIce`:
  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"`
`probabilityCalledHomIfNormal`:
  Object of class `"numeric"`
`probabilityCalledHetIfLoh`:
  Object of class `"numeric"`

### Extends

Class `HmmSnpCopyNumberSet-class`, directly. Class `HmmSnpCallSet-class`, directly. Class `hSet-class`, by class "HmmSnpCopyNumberSet", distance 2. Class `AnnotatedSnpSet-class`, by class "HmmSnpCopyNumberSet", distance 3. Class `AnnotatedSnpCallSet-class`, by class "HmmSnpCopyNumberSet", distance 4. Class `AnnotatedSnpCopyNumberSet-class`, by class "HmmSnpCopyNumberSet", distance 4, with explicit coerce. Class `SnpCallSet-class`, by class "HmmSnpCopyNumberSet", distance 5. Class `class.eSet`, by class "HmmSnpCopyNumberSet", distance 6. Class `VersionedBiobase-class`, by class "HmmSnpCopyNumberSet", distance 7. Class `Versioned-class`, by class "HmmSnpCopyNumberSet", distance 8. Class `SnpCopyNumberSet-class`, by class "HmmSnpCopyNumberSet", distance 5, with explicit coerce. Class `class.eSet`, by class "HmmSnpCopyNumberSet", distance 6, with explicit coerce. Class `VersionedBiobase-class`, by class "HmmSnpCopyNumberSet", distance 7, with explicit coerce. Class `Versioned-class`, by class "HmmSnpCopyNumberSet", distance 8, with explicit coerce. Class `hSet-class`, by class "HmmSnpCallSet", distance 2. Class `AnnotatedSnpSet-class`, by class "HmmSnpCallSet", distance 3. Class `AnnotatedSnpCallSet-class`, by class "HmmSnpCallSet", distance 4. Class `AnnotatedSnpCopyNumberSet-class`, by class "HmmSnpCallSet", distance 4, with explicit coerce. Class `SnpCallSet-class`, by class "HmmSnpCallSet", distance 5. Class `class.eSet`, by class "HmmSnpCallSet", distance 6. Class `VersionedBiobase-class`, by class "HmmSnpCallSet", distance 7. Class `Versioned-class`, by class "HmmSnpCallSet", distance 8. Class `SnpCopyNumberSet-class`, by class "HmmSnpCallSet", distance 5, with explicit coerce. Class `class.eSet`, by class "HmmSnpCallSet", distance 6, with explicit coerce. Class `VersionedBiobase-class`, by class "HmmSnpCallSet", distance 7, with explicit coerce. Class `Versioned-class`, by class "HmmSnpCallSet", distance 8, with explicit coerce.

### Methods

[
  `signature(x = "HmmSnpSet")`: ...
[<-
  `signature(x = "HmmSnpSet")`: ...
breakpoints
  `signature(object = "HmmSnpSet")`: ...
calculateEmissionProbability
  `signature(object = "HmmSnpSet")`: ...
coerce
  `signature(from = "AnnotatedSnpSet", to = "HmmSnpSet")`: ...
callsIce
  `signature(object = "HmmSnpSet")`: ...
copyNumberIce
  `signature(object = "HmmSnpSet")`: ...
getCopyNumberLocation
  `signature(object = "HmmSnpSet")`: ...
getLohProbability
  `signature(object = "HmmSnpSet")`: ...
getTransitionProbability
  `signature(object = "HmmSnpSet")`: ...
hmm
  `signature(object = "HmmSnpSet")`: ...
ice2VanillaICE
  `signature(.Object = "HmmSnpSet")`: Resets the package attribute from ICE (DEPRECATED package name) to VanillaICE
initialize
  `signature(.Object = "HmmSnpSet")`: ...
locationCopyNumber
  `signature(object = "HmmSnpSet")`: ...
locationCopyNumber<-
  `signature(object = "HmmSnpSet")`: ...
plotHmm
  `signature(object = "HmmSnpSet")`: ...
predictions
  `signature(object = "HmmSnpSet")`: ...
predictions<-
  `signature(object = "HmmSnpSet", value = "matrix")`: ...
scaleCopyNumber
  `signature(object = "HmmSnpSet")`: ...
scaleCopyNumber<-
  `signature(object = "HmmSnpSet")`: ...
show
  `signature(object = "HmmSnpSet")`: ...

### Note

### Author(s)

Robert Scharpf

### References

### See Also

`HmmSnpCopyNumberSet-class`, `HmmSnpCallSet-class` `hSet-class`

### Examples

    showClass("HmmSnpSet")

[Package VanillaICE version 1.0.2 Index]