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 |
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
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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"
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