ccPred {BGmix} | R Documentation |
Reads predictive p-values from files output from BGmix. Also (optionally) reads posterior predictive distributions of data.
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)