saps: Significance Analysis of Prognostic Signatures
Version 2.4.2

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.

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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
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("saps")

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...

Functions

calculatePEnrichment Man page
calculatePPure Man page
calculatePRandom Man page
calculateQValue Man page
plotEnrichment Man page
plotKM Man page
plotRandomDensity Man page
plotSapsScoreDensity Man page
rankConcordance Man page
saps Man page
saps-package Man page

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
saps documentation built on Oct. 5, 2016, 4:32 a.m.