plotTrace: Trace plots for BGmix output.

In BGmix: Bayesian models for differential gene expression

Description

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

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.

Author(s)

Alex Lewin

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))

BGmix documentation built on Nov. 8, 2020, 4:54 p.m.