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.

AuthorDaniel Schmolze [aut, cre], Andrew Beck [aut], Benjamin Haibe-Kains [aut]
Date of publicationNone
MaintainerDaniel Schmolze <saps@schmolze.com>
LicenseMIT + file LICENSE
Version2.4.2

View on Bioconductor

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.