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

1 2 3 4 5 6 |

```
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:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
[1] "Output directory is ./run.1"
[1] "got beta"
[1] "got sig2"
[1] "got zg"
```

BGmix documentation built on May 6, 2019, 2:29 a.m.

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