ccPred

0th

Percentile

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.

Aliases
  • ccPred
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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