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)) ##no scaling transitionScale(params) <- matrix(1, length(states(options)), length(states(options))) if(validObject(params)) fit <- hmm(options, params)