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]