TailPP: Tail posterior probability for BGmix output.
In BGmix: Bayesian models for differential gene expression

Description Usage Arguments Value Author(s) References See Also Examples

For differential expression models with unstructured priors (no mixture prior), calculates tail posterior probabality and FDR, and plots a histogram. Uses whole posterior distributions of likelihood parameters (found by 'ccTrace') and posterior means of hyperparameters (found by 'ccParams').

1	TailPP(res, nreps, params, paired=F, alpha=0.05, N = 5000, prec=0.05, p.cut = 0.7, plots = T, plot.pi0=F)

`res`	list object output from 'ccTrace'
`nreps`	vector length 2 containing the number of replicates in each condition
`params`	list object output from 'ccParams'
`paired`	logical. TRUE for paired design, FALSE for unpaired.
`alpha`	parameter of the tail posterior probability (1-alpha/2 quantile)
`N`	simulation size for tail posterior probability under H0
`prec`	parameter used when estimating CDF of tail posterior probability under H0
`p.cut`	calculate FDR only for cutoffs on tail posterior probability > p.cut
`plots`	logical. if TRUE, makes plots of the histogram of tail posterior probability with the null density and of FDR
`plot.pi0`	logical. if TRUE, diagnostic plot of the estimated pi0 at different locations and the median estimate

`tpp`	vector of tail posterior probabilities with parameter alpha, one per gene
`FDR`	(smoothed) estimate of FDR for all (distinct) cutoffs > p.cut
`pi0`	estimated proportion of observations under the null
`pp0`	simulations under the null

Natalia Bochkina

Bochkina N., Richardson S. (2007) Tail posterior probability for inference in pairwise and multiclass gene expression data. Biometrics. http://www.blackwell-synergy.com/doi/abs/10.1111/j.1541-0420.2006.00807.x

FDRplotTailPP,histTailPP,EstimatePi0

 data(ybar, ss)
 nreps <- c(8,8)

## Note this is a very short MCMC run!
## For good analysis need proper burn-in period.
 outdir <- BGmix(ybar, ss, nreps, jstar=-1, nburn=0, niter=100, nthin=1)

 params <- ccParams(outdir)  
 res <-  ccTrace(outdir)
  
 tpp.res <- TailPP(res, nreps, params, plots  = FALSE)
 histTailPP(tpp.res)
 FDRplotTailPP(tpp.res, plot.TP = TRUE)