HmmPredict-class {VanillaICE} | R Documentation

## Class for the hidden Markov model results

### Description

Contains the predictions for the hidden states and a list of breakpoint matrices. Each element in the list corresponds to the breakpoints identified in one sample.

### Objects from the Class

Objects can be created by calls of the form `new("HmmPredict", states, predictions, breakpoints, SnpClass)`.

### Slots

`states`:
  Object of class `character`. Character string of the hidden states.
`predictions`:
  Object of class `matrix`. Matrix of predictions.
`breakpoints`:
  Object of class `list`. List of matrices. Each element is the matrix of breakpoints for one sample.
`SnpClass`:
  Object of class `character`. The class of SNP data (e.g., `oligoSnpSet`)
`featureData`:
  Object of class `AnnotatedDataFrame`

### Methods

SnpClass
  `signature(object = "HmmPredict")`: Accessor for class of SNP data
[
  `signature(x = "HmmPredict")`: Subsetting the predictions
breakpoints
  `signature(object = "HmmPredict")`: Accessor for the list of breakpoints
breakpoints<-
  `signature(object = "HmmPredict", value = "data.frame")`: Replacement method for breakpoints
fData
  `signature(object="HmmPredict")`: Accessor for the data frame of all feature-level (SNP-level) annotation (e.g., physical position)
featureData
  `signature(object = "HmmPredict")`: Accessor for the featureData
featureNames
  `signature(object = "HmmPredict")`: Character string of SNP identifiers
getPar
  `signature(object = "HmmPredict")`: Graphical parameters.
initialize
  `signature(.Object = "HmmPredict")`
position
  `signature(object = "HmmPredict")`: Accessor for the physical position of SNPs in the object `HmmPredict`
predictions
  `signature(object = "HmmPredict")`: Accessor for the predictions
predictions<-
  `signature(object = "HmmPredict", value="matrix")`: Replacement method for predictions
sampleNames
  `signature(object = "HmmPredict")`: Sample names
show
  `signature(object = "HmmPredict")`
states
  `signature(object = "HmmPredict")`: Accessor for hidden states

### Author(s)

R. Scharpf

### See Also

`hmm`

### Examples

    showClass("HmmPredict")

[Package VanillaICE version 1.4.0 Index]