ccSummary {BGmix}R Documentation

Read summary of BGmix output

Description

Reads the summary.txt file output by BGmix, containing information about data sets used and model options. This function is called by ccParams, ccTrace and ccPred, therefore users will not in general need to call it directly.

Usage

ccSummary(filedir)

Arguments

filedir character. The name of the output directory created by BGmix.

Value

A list of scalar values, as follows:

ngenes,nconds,neffects,ncomps,ntau nos. genes, conditions, effects, mixture components, gene variances
jstar label of effect with mixture prior (labels start at 0)
move.choice.bz,move.choice.cut,move.choice.aa, move.choice.eta,move.choice.lam,move.choice.tau, like.choice,trace.out,trace.pred model choice options (see BGmix help for details
lambda.up.init,lambda.down.init, eta.up.init,eta.down.init inital values for eta and lambda (parameters of mixture components)

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)
summ <- ccSummary(outdir)

[Package BGmix version 1.2.0 Index]