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 |

**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...

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

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