trace.plot: Trace plot for 'RJaCGH' object

In RJaCGH: Reversible Jump MCMC for the Analysis of CGH Arrays

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

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.

Value

A plot is drawn.

Author(s)

Oscar M. Rueda and Ramon Diaz

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")

Example output

 Doing Array  array1 
    Starting Reversible Jump
       Start burn-in
       End burn-in

RJaCGH documentation built on May 2, 2019, 3:34 p.m.