| hmm {VanillaICE} | R Documentation |
Fits the hidden Markov model
hmm(object, params)
object |
An object of class HmmOptions |
params |
An object of class HmmParameter |
None yet.
An object of class HmmPredict
R. Scharpf
RB Scharpf et al. (2008) Hidden Markov Models for the assessment of chromosomal alterations using high-throughput SNP arrays, Annals of Applied Statistics
HmmParameter-class
HmmPredict-class
SnpLevelSet-class
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))
transitionScale(params) <- scaleTransitionProbability(options)
validObject(params)
fit <- hmm(options, params)