calcFDR: Estimate the FDR (false discovery rate) and related...
In BGmix: Bayesian models for differential gene expression

Description Usage Arguments Details Value Author(s) Examples

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. Estimated numbers of false positives and false negatives are also output.

1	calcFDR(res, pcut = seq(0.01,0.5,0.01), true.z = NULL, q.print = F)

`res`	list object output from ccParams (this includes the posterior classification probabilities)
`pcut`	scalar or vector of thresholds for which to estimate FDR etc.
`true.z`	vector of true classifications (if known, eg. for simulated data)
`q.print`	Print FDR etc. when pcut is a vector?

If the true classification is known, it can be given as true.z, and the true FDR etc. for the threshold probability can be calculated.

`fdr.est, fnr.est`	scalars or vectors of estimated FDR, FNR
`fp.est, fn.est`	scalars or vectors of estimated no. false positives, no. false negatives
`fdr.true, fnr.true`	scalars or vectors of true FDR, FNR
`fp.true, fn.true`	scalars or vectors of true no. false positives, no. false negatives
`npos, nneg`	scalars or vectors of no. declared positives, no. declared negatives
`prob.class`	posterior classification probabilites (from the 'res' object input to this function)
`true.z`	argument to function is output
`pcut`	argument to function is output

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)

Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
[1] "Mixture prior on comp. 2"
[1] "delta ~ Gamma, MH"
[1] "eta (scale of Gamma) updated"
[1] "lambda (shape of Gamma) not updated"
[1] "Normal Likelihood"
[1] "tau ~ Gamma"
[1] "a (prior for tau) is updated"
[1] "trace output for parameters"
[1] "no trace for predicted data"
 Burn-in: 

 Main up-dates: 
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[1] "Output directory is ./run.1"
[1] "got beta"
[1] "got sig2"
[1] "got zg"