FDRplotTailPP: Plot of FDR for tail posterior probability

In BGmix: Bayesian models for differential gene expression

Description

Plots smoothed FDR vs tail posterior probability or vs the number of differentially expressed (DE) genes

Usage

FDRplotTailPP(tpp.res, nmax = sum(! is.na(tpp.res$FDR)), plot.TP = F)

Arguments

tpp.res	output of TailPP
nmax	maximum size of the list of DE genes
plot.TP	logical. If TRUE FDR is plotted, otherwise the number of false positives is plotted vs the number of differentially expressed genes

Author(s)

Natalia Bochkina

References

Bochkina N., Richardson S. (2007) Tail posterior probability for inference in pairwise and multiclass gene expression data. Biometrics.

See Also

TailPP, histTailPP,EstimatePi0

Examples

 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)
 FDRplotTailPP(tpp.res, plot.TP = TRUE)

BGmix documentation built on Nov. 8, 2020, 4:54 p.m.