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)