RJaCGH (version 2.0.4)

modelAveraging: Method for model averaging for RJaCGH objects.

Description

Bayesian model averaging for the estimation of hidden state sequence.

Usage

modelAveraging(obj, array=NULL, Chrom=NULL)
## S3 method for class 'RJaCGH':
modelAveraging(obj, array=NULL, Chrom=NULL)

Arguments

obj

An object of corresponding class

array

Array to be used. If NULL, all of them are used.

Chrom

Vector of chromosomes to be used. If NULL, all of them are used.

Value

• states
  Factor with the hidden state sequence
• prob.states
  Matrix with the probabilities associated to every states for every observation.

Details

With the posterior distribution of the number of hidden states, bayesian model averaging is performed on every model using states method.

As the other methods, it may return a list with sublists according to the hierarchy of RJaCGH objects.

References

Rueda OM, Diaz-Uriarte R. Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH. PLoS Comput Biol. 2007;3(6):e122

See Also

RJaCGH, summary.RJaCGH, states, plot.RJaCGH, trace.plot

Examples

y <- c(rnorm(100, 0, 1), rnorm(10, -3, 1), rnorm(20, 3, 1),
       rnorm(100,0, 1)) 
Pos <- sample(x=1:500, size=230, replace=TRUE)
Pos <- cumsum(Pos)
Chrom <- rep(1:23, rep(10, 23))

jp <- list(sigma.tau.mu=rep(0.5, 5), sigma.tau.sigma.2=rep(0.3, 5),
sigma.tau.beta=rep(0.7, 5), tau.split.mu=0.5, tau.split.beta=0.5)
fit.genome <- RJaCGH(y=y, Pos=Pos, Chrom=Chrom, model="Genome",
burnin=1000, TOT=10000, jump.parameters=jp, max.k=5)
mo <- modelAveraging(fit.genome)
print(mo)