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.

Version: 1.0.0
Depends: R (≥ 2.14.0), survival
Imports: piano, survcomp, reshape2
Suggests: snowfall, knitr
Published: 2014-10-08
Author: Daniel Schmolze [aut, cre], Andrew Beck [aut], Benjamin Haibe-Kains [aut]
Maintainer: Daniel Schmolze <saps at>
License: MIT + file LICENSE
NeedsCompilation: no
Materials: NEWS
CRAN checks: saps results


Reference manual: saps.pdf
Vignettes: SAPS Vignette
Package source: saps_1.0.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
OS X Snow Leopard binaries: r-release: not available, r-oldrel: not available
OS X Mavericks binaries: r-release: not available