getSequence {RJaCGH}R Documentation

Viterbi path from every MCMC sample

Description

This function creates files with the maximum a posteriory (Viterbi) sequence of hidden states for every MCMC sample.

Usage

getSequence(obj, filename, alteration)

Arguments

obj An object of class 'RJaCGH', 'RJaCGH.genome' or 'RJaCGH.Chrom'
filename A string with a name for the file(s) to be created. See details.
alteration Either 'Gain' or 'Loss'

Details

'k' files are created (where 'k' is the number of different models fitted in 'obj') in the working directory. Each file contains as many rows as MCMC samples for that model. Each row describes the hidden state sequence, in the format 'state', 't', 'breakpoint position', etc. until a '-1' showing the end of the sequence and a final number, the times that that particular path has occurred in the MCMC.

Value

'k' files are created with names 'filename' plus the number of the model (in fact, the number of hidden states in that model.

Author(s)

Oscar M. Rueda and Ramon Diaz Uriarte

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, link{pMCR}, link{prob.seq}, pREC_A, pREC_S

Examples

## Not run: 
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, 4), sigma.tau.sigma.2=rep(0.3, 4),
           sigma.tau.beta=rep(0.7, 4), tau.split.mu=0.5, tau.split.beta=0.5)

fit.genome <- RJaCGH(y=y, Pos=Pos, Chrom=Chrom, model="genome",
                    burnin=10, TOT=1000, k.max = 4,
                    jump.parameters=jp)
getSequence(fit.genome, 'sequence', 'Gain')
## End(Not run)

[Package RJaCGH version 1.2.5 Index]