ccTrace: Read trace files from BGmix

In BGmix: Bayesian models for differential gene expression

Description

Reads output files containing whole posterior distributions from BGmix. Also calls 'ccSummary', and outputs model options.

Usage

ccTrace(filedir, q.beta = T, q.sig = T, q.z = T, quiet = T)

Arguments

filedir	character. The name of the output directory created by BGmix.
q.beta	logical. Read beta values?
q.sig	logical. Read gene variances?
q.z	logical. Read z values?
quiet	logical. Parameter passed to 'scan'. (If false, 'scan' prints details of number of items read in.)

Value

summ	list object output by 'ccSummary'
eta	matrix (no. components -1) x no. MCMC samples. Posterior of mixture component parameters (eta).
lambda	matrix (no. components -1) x no. MCMC samples. Posterior of mixture component parameters (lambda).
aa	matrix no. MCMC samples x no. variances. Posterior of variance hyperparameters (a).
bb	matrix no. MCMC samples x no. variances. Posterior of variance hyperparameters (b).
wtc	matrix no. MCMC samples x no. mixture components. Posterior of mixture weights.
beta	matrix no. effects x no. genes x no. MCMC samples. Posterior of gene effects.
sig2	matrix no. variances x no. genes x no. MCMC samples. Posterior of gene variances.
zg	matrix no. MCMC samples x no. genes. Posterior of gene allocations.

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)

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