| 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
Rueda OM, Diaz-Uriarte R. Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH. PLoS Comput Biol. 2007;3(6):e122
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)