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]