plotTrace

0th

Percentile

Trace plots for BGmix output.

Trace plots are plotted for all scalar parameters. Optionally, traces are plotted for parameters indexed by genes, but for selected genes only.

Keywords
hplot
Usage
plotTrace(res, q.beta = T, q.sig = T, q.z = T, ind.genes = (1:3))
Arguments
res
list object output from 'ccTrace'
q.beta
logical. Plot trace of beta (gene effect) parameters?
q.sig
logical. Plot trace of gene variances?
q.z
logical. Plot trace of gene allocation parameters?
ind.genes
indices of genes for which to plot gene parameters.
Aliases
  • plotTrace
Examples
## Note this is a very short MCMC run!
## For good analysis need proper burn-in period.
data(ybar,ss)
outdir <- BGmix(ybar, ss, c(8,8), nburn=0, niter=100, nthin=1)
tr <- ccTrace(outdir)
plotTrace(tr)
plotTrace(tr,q.beta=TRUE,q.sig=FALSE,q.z=FALSE,ind.genes=1)
plotTrace(tr,q.beta=FALSE,q.sig=FALSE,q.z=TRUE,ind.genes=sample(1:1000,5))
Documentation reproduced from package BGmix, version 1.32.0, License: GPL-2

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