HmmOptions-class {VanillaICE}R Documentation

Class "HmmOptions"

Description

Options for fitting the hidden Markov model.

Objects from the Class

Objects can be created by calls of the form new("HmmOptions", snpset, states, copyNumber.location, copyNumber.scale, copyNumber.ICE, calls.ICE, probHomCall, term5).

Slots

states:
Object of class "character". Hidden states of the HMM.
snpset:
"SnpLevelSet" instance.
copyNumber.location:
Object of class "numeric". Ignored when snpset is an instance of SnpCallSet. See copyNumber.location
copyNumber.scale:
Object of class "NULLOrNumeric". This slot is not currently used. If one has standard errors for the copy number estimates, the inverse of the standard errors should be stored in the cnConfidence assayData element of the snpset object.
copyNumber.ICE:
Object of class "logical". See copyNumber.ICE.
calls.ICE:
Object of class "logical". See calls.ICE
probHomCall:
Object of class "numeric". The probability of a homozygous genotype call corresponding to each of the states. When calls.ICE is TRUE, only the first two elements will be used.
term5:
Object of class "NULLOrNumeric". User-specified probabilities of f(HOM | genotype call, state). Ignored when calls.ICE is FALSE. For more details, see Equation 2.7 in the manuscript that this package references.

Methods

[
signature(x = "HmmOptions"):
annotation
signature(object = "HmmOptions"):
annotation<-
signature(object = "HmmOptions", value = "ANY"):
calculateDistance
signature(object = "HmmOptions"):
calls.ICE
signature(object = "HmmOptions"):
calls.ICE<-
signature(object = "HmmOptions", value="logical"):
copyNumber.ICE
signature(object = "HmmOptions"):
copyNumber.ICE<-
signature(object = "HmmOptions", value="logical"):
db
signature(object = "HmmOptions"):
hmm
signature(object = "HmmOptions", params = "HmmParameter"):
initialize
signature(.Object = "HmmOptions"):
notes
signature(object = "HmmOptions"):
show
signature(object = "HmmOptions"):
states
signature(object = "HmmOptions"):
states<-
signature(object = "HmmOptions", value = "character"):

Author(s)

R. Scharpf

See Also

HmmParameter-class

Examples

showClass("HmmOptions")

[Package VanillaICE version 1.4.0 Index]