hSet-class {VanillaICE}R Documentation

Virtual class for fitting HMMs to SNP chip data

Description

Objects from the Class

A virtual Class: No objects may be created from it.

Slots

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"

Extends

Class AnnotatedSnpSet-class, directly. Class AnnotatedSnpCallSet-class, by class "AnnotatedSnpSet", distance 2. Class AnnotatedSnpCopyNumberSet-class, by class "AnnotatedSnpSet", distance 2, with explicit coerce. Class SnpCallSet-clas, by class "AnnotatedSnpSet", distance 3. Class class.eSet, by class "AnnotatedSnpSet", distance 4. Class VersionedBiobase-class, by class "AnnotatedSnpSet", distance 5. Class Versioned-class, by class "AnnotatedSnpSet", distance 6. Class SnpCopyNumberSet-class, by class "AnnotatedSnpSet", distance 3, with explicit coerce. Class class.eSet, by class "AnnotatedSnpSet", distance 4, with explicit coerce. Class VersionedBiobase-class, by class "AnnotatedSnpSet", distance 5, with explicit coerce. Class Versioned-class, by class "AnnotatedSnpSet", distance 6, with explicit coerce.

Methods

chromosomeArm
signature(object = "hSet")
chromosomeArm<-
signature(object = "hSet")
distance
signature(object = "hSet")
distance<-
signature(object = "hSet")
emissionProbability
signature(object = "hSet")
emissionProbability<-
signature(object = "hSet")
hmmBySample
signature(object = "hSet")
initialStateProbability
signature(object = "hSet")
initialStateProbability<-
signature(object = "hSet")
likelihood
signature(object = "hSet")
likelihood<-
signature(object = "hSet")
numberStates
signature(object = "hSet")
stateNames
signature(object = "hSet")
stateNames<-
signature(object = "hSet")
transitionProbability
signature(object = "hSet")
transitionProbability<-
signature(object = "hSet")
viterbi
signature(object = "hSet")

Note

Author(s)

References

Robert Scharpf

See Also

HmmSnpSet-class, HmmSnpCopyNumberSet-class, HmmSnpCallSet-class

Examples

showClass("hSet")

[Package VanillaICE version 1.0.2 Index]