summary.RJaCGH {RJaCGH} | R Documentation |
'summary' method for objects of class 'RJaCGH', 'RJaCGH.Chrom', 'RJaCGH.genome' and 'RJaCGH.array'.
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", ...)
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. |
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
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 |
Oscar Rueda and Ramon Diaz Uriarte
Oscar Rueda and Ramon Diaz Uriarte, in prep.
RJaCGH
,
states
, model.averaging
,
plot.RJaCGH
, trace.plot
,
gelman.brooks.plot
, collapseChain
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)