BGmix (version 1.32.0)

plotPredChecks: Plots of predictive checks for mixture prior.

Description

Histograms and q-q plots of predictive p-values for the mixture prior. Separate plots are given for each mixture component, using only genes with high posterior probability of being classified into the relevant component.

Usage

plotPredChecks(pvals, pc, probz = 0.8, label = "", breaks = 20)

Arguments

pvals

matrix of predictive p-values output by 'ccPred' (NB, not the whole list object, just the matrix of p-values)

pc

matrix of posterior classification probabilities output by 'ccParams' (NB, not the whole list object, just the matrix of probabilities)

probz

threshold on posterior probabilities for including genes in each mixture component plot

label

title used on histograms

breaks

argument input to histogram

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)
params <- ccParams(outdir)
pred <- ccPred(outdir)
plotPredChecks(pred$pval.ybar.mix2,params$pc,probz=0.5)