plotPredChecks

0th

Percentile

Plots of predictive checks for mixture prior.

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.

Keywords
hplot
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
Aliases
  • plotPredChecks
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)
Documentation reproduced from package BGmix, version 1.32.0, License: GPL-2

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