# gprege: Gaussian Process Ranking and Estimation of Gene Expression time-series

The gprege package implements the methodology described in Kalaitzis & Lawrence (2011) "A simple approach to ranking differentially expressed gene expression time-courses through Gaussian process regression". The software fits two GPs with the an RBF (+ noise diagonal) kernel on each profile. One GP kernel is initialised wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimised via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance. The log-ratio of marginal likelihoods of the two hypotheses acts as a score of differential expression for the profile. Comparison via ROC curves is performed against BATS (Angelini et.al, 2007). A detailed discussion of the ranking approach and dataset used can be found in the paper (http://www.biomedcentral.com/1471-2105/12/180).

- Author
- Alfredo Kalaitzis <alkalait@gmail.com>
- Date of publication
- None
- Maintainer
- Alfredo Kalaitzis <alkalait@gmail.com>
- License
- AGPL-3
- Version
- 1.18.0
- URLs

## Man pages

- compareROC
- Make ROC plots.
- DellaGattaData
- Fragment dataset of 13 time-point mouse microarray time...
- demTp63Gp1
- gprege on TP63 expression time-series.
- DGdat_p63
- BATS rankings (Angelini, 2007) Case 1: Delta error prior Case...
- exhaustivePlot
- Plot of the LML function by exhaustive search.
- gprege
- Gaussian process ranking and estimation of gene expression...
- gprege-package
- gprege - Gaussian Process Ranking and Estimation of Gene...
- rocStats
- Make ROC curve data.

## Files in this package

gprege/DESCRIPTION |

gprege/NAMESPACE |

gprege/R |

gprege/R/compareROC.R |

gprege/R/demTp63Gp1.R |

gprege/R/exhaustivePlot.R |

gprege/R/gprege.R |

gprege/R/rocStats.R |

gprege/build |

gprege/build/vignette.rds |

gprege/data |

gprege/data/DGdat_p63.RData |

gprege/data/FragmentDellaGattaData.RData |

gprege/data/FullDellaGattaData.RData |

gprege/data/datalist |

gprege/inst |

gprege/inst/CITATION |

gprege/inst/NEWS |

gprege/inst/doc |

gprege/inst/doc/gprege_quick.R |

gprege/inst/doc/gprege_quick.Rnw |

gprege/inst/doc/gprege_quick.bib |

gprege/inst/doc/gprege_quick.pdf |

gprege/man |

gprege/man/DGdat_p63.Rd |

gprege/man/DellaGattaData.Rd |

gprege/man/compareROC.Rd |

gprege/man/demTp63Gp1.Rd |

gprege/man/exhaustivePlot.Rd |

gprege/man/gprege-package.Rd |

gprege/man/gprege.Rd |

gprege/man/rocStats.Rd |

gprege/vignettes |

gprege/vignettes/gprege_quick.Rnw |

gprege/vignettes/gprege_quick.bib |