saps: Significance Analysis of Prognostic Signatures

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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

View on Bioconductor

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