hmm {VanillaICE}R Documentation

Fits the hidden Markov model

Description

Fits the hidden Markov model

Usage

hmm(object, params)

Arguments

object An object of class HmmOptions
params An object of class HmmParameter

Details

None yet.

Value

An object of class HmmPredict

Author(s)

R. Scharpf

References

RB Scharpf et al. (2008) Hidden Markov Models for the assessment of chromosomal alterations using high-throughput SNP arrays, Annals of Applied Statistics

See Also

HmmParameter-class HmmPredict-class SnpLevelSet-class

Examples

data(chromosome1)
chromosome1 <- chromosome1[1:500, ]
options <- new("HmmOptions",
               states=c("D", "N", "L", "A"),
               snpset=chromosome1,
               copyNumber.location=c(1, 2, 2, 3),
               probHomCall=c(0.99, 0.7, 0.99, 0.7))
validObject(options)
params <- new("HmmParameter", 
              states=states(options),
              initialStateProbability=0.99)
cn.emission <- copyNumber.emission(options)
gt.emission <- calls.emission(options)
emission(params) <- cn.emission + gt.emission ##log scale
genomicDistance(params) <- exp(-2 *calculateDistance(options)/(100*1e6))
##no scaling
transitionScale(params) <- matrix(1, length(states(options)), length(states(options)))
if(validObject(params)) fit <- hmm(options, params)

[Package VanillaICE version 1.4.0 Index]