plotFDR {BGmix} | R Documentation |
Given a threshold on the posterior probabilities, genes are declared as null or differentially expressed. For any given threshold, the FDR (false discovery rate) and FNR (false non-discovery rate) can be estimated using the posterior probabilities. This function plots these quantities twice, once versus the threshold probabilities, and once versus the number of declared positives.
plotFDR(res, ylim = NULL, q.plotfnr = F, q.plotpcut = T, q.plotnpos = T, ...)
res |
list object output from 'calcFDR' |
ylim |
optional argument specifying limit for y-axis |
q.plotfnr |
Include FNR in plots? |
q.plotpcut |
Include the plot of error rates v. threshold on posterior probabilites? |
q.plotnpos |
Include the plot of error rates v. no. positives. |
... |
arguments passed to 'plot' |
No value is returned to R. Results from BGmix model are output to files.
Alex Lewin
## 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) fdr <- calcFDR(params) par(mfrow=c(1,2)) plotFDR(fdr)