HmmSnpCopyNumberSet-class {VanillaICE}R Documentation

HmmSnpCopyNumberSet

Description

Objects from the Class

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

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"
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"
copyNumberIce:
Object of class "logical"

Extends

Class hSet-class, directly. Class AnnotatedSnpSet-class, by class "hSet", distance 2. Class AnnotatedSnpCallSet-class, by class "hSet", distance 3. Class AnnotatedSnpCopyNumberSet-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 = "HmmSnpCopyNumberSet")
calculateEmissionProbability
signature(object = "HmmSnpCopyNumberSet")
coerce
signature(from = "AnnotatedSnpSet", to = "HmmSnpCopyNumberSet")
copyNumberIce
signature(object = "HmmSnpCopyNumberSet")
getCopyNumberLocation
signature(object = "HmmSnpCopyNumberSet")
getTransitionProbability
signature(object = "HmmSnpCopyNumberSet")
hmm
signature(object = "HmmSnpCopyNumberSet")
locationCopyNumber
signature(object = "HmmSnpCopyNumberSet")
locationCopyNumber<-
signature(object = "HmmSnpCopyNumberSet")
plotHmm
signature(object = "HmmSnpCopyNumberSet")
predictions
signature(object = "HmmSnpCopyNumberSet")
predictions<-
signature(object = "HmmSnpCopyNumberSet", value = "ANY")
scaleCopyNumber
signature(object = "HmmSnpCopyNumberSet")
scaleCopyNumber<-
signature(object = "HmmSnpCopyNumberSet")
show
signature(object = "HmmSnpCopyNumberSet")

Note

Author(s)

Robert Scharpf

References

See Also

HmmSnpSet-class, HmmSnpCallSet-class hSet-class

Examples

showClass("HmmSnpCopyNumberSet")

[Package VanillaICE version 1.0.2 Index]