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]