# ccPred

From BGmix v1.32.0
by Alex Lewin

##### Read predictive quantities output from BGmix.

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

- Keywords
- manip

##### Usage

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

##### Arguments

- 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.)

##### Value

- 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.

##### Note

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.

##### 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)
pred <- ccPred(outdir)
```

*Documentation reproduced from package BGmix, version 1.32.0, License: GPL-2*

### Community examples

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