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 1.2.0 Index]