RJaCGH (version 2.0.4)

trace.plot: Trace plot for 'RJaCGH' object

Description

A trace plot with the trajectory of the Markov Chain.

Usage

trace.plot(x, k = NULL, array = NULL, Chrom = NULL, main.text = NULL)

Arguments

x

any of RJaCGH, RJaCGH.Chrom, RJaCGH.Genome, RJaCGH.array objects

k

Model to plot (i.e., number of hidden states). If NULL, the most visited is taken.

array

the name of the array to plot.

Chrom

the number of the chromosome to plot.

main.text

Main text of the plot

Value

A plot is drawn.

Details

This is simply a call to matplot to show the values sampled in the chain.

The colors does not correspond to any particular level of gain/loss.

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, modelAveraging, plot.RJaCGH, states,

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=10, TOT=100, jump.parameters=jp, k.max = 5)
trace.plot(fit.genome, array="array1")