| collapseChain {RJaCGH} | R Documentation |
method to join or collapse several 'RJaCGH' objects, for use in every method of class 'RJaCGH'.
collapseChain(obj) ## S3 method for class 'RJaCGH': collapseChain(obj) ## S3 method for class 'RJaCGH.genome': collapseChain(obj) ## S3 method for class 'RJaCGH.Chrom': collapseChain(obj) ## S3 method for class 'RJaCGH.array': collapseChain(obj)
obj |
a list containing several parallel chains; that is objects of any of RJaCGH, RJaCGH.Chrom, RJaCGH.genome, RJaCGH.array classes (obviously, all of the same class). |
If several parallel chains are run and if they converge (see
gelman.brooks.plot) they should be joined in one. This is
what this method does.
Please note that this function returns only one object, so one can not
call later gelman.brooks.plot.
An object of the same class as any of the list obj.
Oscar M. Rueda and Ramon Diaz Uriarte
Oscar M. Rueda and Ramon Diaz Uriarte. A flexible, accurate and extensible statistical method for detecting genomic copy-number changes. http://biostats.bepress.com/cobra/ps/art9/. {http://biostats.bepress.com/cobra/ps/art9/}.
RJaCGH,
summary.RJaCGH, model.averaging,
plot.RJaCGH, states,
trace.plot, collapseChain
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, 4), sigma.tau.sigma.2=rep(0.3, 4),
sigma.tau.beta=rep(0.7, 4), tau.split.mu=0.5, tau.split.beta=0.5)
fit.chrom <- RJaCGH(y=y, Pos=Pos, Chrom=Chrom, model="Chrom",
burnin=10, TOT=1000, k.max = 4,
jump.parameters=jp)
fit.genome <- list()
for (i in 1:4) {
fit.genome[[i]] <- RJaCGH(y=y, Pos=Pos, Chrom=Chrom, model="genome",
burnin=10, TOT=1000, jump.parameters=jp, k.max = 4)
}
## Not run: gelman.brooks.plot(fit.genome)
##If all R seem to be round 1
## Not run: fit.genome <- collapseChain(fit.genome)