ccSummary: Read summary of BGmix output

Description Usage Arguments Value Author(s) Examples

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

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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

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## 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)


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