summary.RJaCGH {RJaCGH} | R Documentation |
'summary' method for objects of class 'RJaCGH'.
## S3 method for class 'RJaCGH': summary(object, array=NULL, Chrom=NULL, k = NULL, point.estimator = "median", quantiles=NULL, ...)
object |
RJaCGH objects |
array |
vector of names of arrays to summarize. If NULL, all of them. |
Chrom |
vector of chromosomes to summarize. If NULL, all of them. |
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". |
quantiles |
A vector of probabilities for the quantiles of the posterior distribution of means and variances. |
... |
Additional arguments passed to summary. |
Depending of the arguments passed, 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
k |
Frequencies of the hidden states visited by the sampler. |
mu |
Quantiles of the posterior distribution of mu |
sigma.2 |
Quantiles of the posterior distribution of sigma.2 |
beta |
Point estimator of beta |
stat |
Initial distribution of the hidden states. |
Oscar M. Rueda and Ramon Diaz Uriarte
Rueda OM, Diaz-Uriarte R. Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH. PLoS Comput Biol. 2007;3(6):e122
RJaCGH
,
states
, modelAveraging
,
plot.RJaCGH
, trace.plot
,
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.chrom <- RJaCGH(y=y, Pos=Pos, Chrom=Chrom, model="Chrom", burnin=10, TOT=100, jump.parameters=jp, k.max = 5) summary(fit.chrom)