summary.RJaCGH {RJaCGH}R Documentation

Summarizing RJaCGH models

Description

'summary' method for objects of class 'RJaCGH', 'RJaCGH.Chrom', 'RJaCGH.genome' and 'RJaCGH.array'.

Usage

summary.RJaCGH(object, k = NULL, point.estimator = "median", ...)
summary.RJaCGH.Chrom(object, point.estimator="median", ...)
summary.RJaCGH.genome(object, k=NULL, point.estimator="median", ...)
summary.RJaCGH.array(object, point.estimator="median", ...)

Arguments

object any of RJaCGH, RJaCGH.Chrom, RJaCGH.genome, RJaCGH.array objects
k Model to summarize (i.e., number of hidden states). If NULL, the most visited is taken.
point.estimator Type of point estimator for mu, sigma.2 and beta. It can be "mean", "median" or "mode".
... Additional arguments passed to summary.

Details

Depending of the type of object, a list with contains sublists can be returned, similarly to RJaCGH and similar objects of the family. The point estimator "mode" is simply the max value obtained in a kernel density estimation through the function density

Value

y y values
x x values (distances between genes)
mu Point estimator of mu
sigma.2 Point estimator of sigma.2
beta Point estimator of beta

Author(s)

Oscar Rueda and Ramon Diaz Uriarte

References

Oscar Rueda and Ramon Diaz Uriarte, in prep.

See Also

RJaCGH, states, model.averaging, plot.RJaCGH, trace.plot, gelman.brooks.plot, collapseChain

Examples

y <- c(rnorm(100, 0, 1), rnorm(10, -3, 1), rnorm(20, 3, 1), rnorm(100,
0, 1))
Pos <- runif(230)
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.chrom <- RJaCGH(y=y, Pos=Pos, Chrom=Chrom, model="Chrom",
burnin=10, TOT=100, jump.parameters=jp, k.max = 5)
summary(fit.chrom)

[Package RJaCGH version 0.4 Index]