ccPred: Read predictive quantities output from BGmix.
In BGmix: Bayesian models for differential gene expression

Description Usage Arguments Value Note Author(s) Examples

Reads predictive p-values from files output from BGmix. Also (optionally) reads posterior predictive distributions of data.

1	ccPred(filedir, q.partial = T, q.trace = F, quiet = T)

`filedir`	character. The name of the output directory created by BGmix.
`q.partial`	logical. Read partial predictive p-values?
`q.trace`	logical. Read posterior predictive distributions of data?
`quiet`	logical. Parameter passed to 'scan'. (If false, 'scan' prints details of number of items read in.)

`pval.ss.post`	matrices no. genes x no. conditions. Posterior predictive p-values for sum of squares for each gene in each condition.
`pval.ss.mix`	matrices no. genes x no. conditions. Mixed predictive p-values for sum of squares for each gene in each condition.
`pval.ss.part`	matrices no. genes x no. conditions. Partial predictive p-values for sum of squares for each gene in each condition.
`pval.ybar.post`	matrices no. genes x no. mixture components. Posterior predictive p-values for ybar for each gene in each mixture component.
`pval.ybar.mix2`	matrices no. genes x no. mixture components. Mixed predictive p-values for ybar for each gene in each mixture component.
`pval.ybar.part`	matrices no. genes x no. mixture components. Partial predictive p-values for ybar for each gene in each mixture component.
`ybar.pred1`	Posterior predictive distribution of ybar.
`ybar.pred3`	Mixed predictive distribution of ybar.
`ss.pred1`	Posterior predictive distribution of sums of squares.
`ss.pred2`	Mixed predictive distribution of sums of squares.

Additional output: pval.ybar.mix1 and pval.ybar.mix3 are alternative versions of mixed predictive p-values (currently not used). Also, ybar.pred2 and ybar.pred4 are the corresponding alternative mixed predictive distributions for ybar.

Alex Lewin

## 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)
pred <- ccPred(outdir)