# saps: Significance Analysis of Prognostic Signatures

Functions implementing the Significance Analysis of Prognostic Signatures method (SAPS). SAPS provides a robust method for identifying biologically significant gene sets associated with patient survival. Three basic statistics are computed. First, patients are clustered into two survival groups based on differential expression of a candidate gene set. P_pure is calculated as the probability of no survival difference between the two groups. Next, the same procedure is applied to randomly generated gene sets, and P_random is calculated as the proportion achieving a P_pure as significant as the candidate gene set. Finally, a pre-ranked Gene Set Enrichment Analysis (GSEA) is performed by ranking all genes by concordance index, and P_enrich is computed to indicate the degree to which the candidate gene set is enriched for genes with univariate prognostic significance. A SAPS_score is calculated to summarize the three statistics, and optionally a Q-value is computed to estimate the significance of the SAPS_score by calculating SAPS_scores for random gene sets.

- Author
- Daniel Schmolze [aut, cre], Andrew Beck [aut], Benjamin Haibe-Kains [aut]
- Date of publication
- None
- Maintainer
- Daniel Schmolze <saps@schmolze.com>
- License
- MIT + file LICENSE
- Version
- 2.4.2

## Man pages

- calculatePEnrichment
- Compute P_enrichment
- calculatePPure
- Compute P_pure
- calculatePRandom
- Compute P_random
- calculateQValue
- Compute saps q-value
- plotEnrichment
- Plot concordance indices for a geneset
- plotKM
- Plot Kaplan-Meier curves for a gene set
- plotRandomDensity
- Draw density plot of 'p_pure' values for random gene sets
- plotSapsScoreDensity
- Draw density plot of 'saps_score' values for random gene sets
- rankConcordance
- Compute concordance indices
- saps
- Compute SAPS statistics
- saps-package
- Implements Significance Analysis of Prognostic Signatures...

## Files in this package

saps/DESCRIPTION |

saps/LICENSE |

saps/NAMESPACE |

saps/NEWS |

saps/R |

saps/R/plots.R |

saps/R/saps.R |

saps/build |

saps/build/vignette.rds |

saps/inst |

saps/inst/doc |

saps/inst/doc/saps.R |

saps/inst/doc/saps.Rmd |

saps/inst/doc/saps.html |

saps/man |

saps/man/calculatePEnrichment.Rd |

saps/man/calculatePPure.Rd |

saps/man/calculatePRandom.Rd |

saps/man/calculateQValue.Rd |

saps/man/plotEnrichment.Rd |

saps/man/plotKM.Rd |

saps/man/plotRandomDensity.Rd |

saps/man/plotSapsScoreDensity.Rd |

saps/man/rankConcordance.Rd |

saps/man/saps-package.Rd |

saps/man/saps.Rd |

saps/vignettes |

saps/vignettes/saps.Rmd |