ccSummary

0th

Percentile

Read summary of BGmix output

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.

Keywords
manip
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)

Aliases
  • ccSummary
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)
Documentation reproduced from package BGmix, version 1.32.0, License: GPL-2

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