plotFDR

0th

Percentile

Plot estimated FDR etc. for BGmix output.

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.

Keywords
hplot
Usage
plotFDR(res, ylim = NULL, q.plotfnr = F, q.plotpcut = T, q.plotnpos = T, ...)
Arguments
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'
Value

No value is returned to R. Results from BGmix model are output to files.

Aliases
  • plotFDR
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)
fdr <- calcFDR(params)
par(mfrow=c(1,2))
plotFDR(fdr)
Documentation reproduced from package BGmix, version 1.32.0, License: GPL-2

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