To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("saps")

In most cases, you don't need to download the package archive at all.

saps

 

   

Significance Analysis of Prognostic Signatures

Bioconductor version: Release (3.3)

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]

Maintainer: Daniel Schmolze <saps at schmolze.com>

Citation (from within R, enter citation("saps")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("saps")

Documentation

HTML R Script SAPS Vignette
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews BiomedicalInformatics, DifferentialExpression, GeneExpression, GeneSetEnrichment, Software, Survival
Version 2.4.2
In Bioconductor since BioC 3.1 (R-3.2) (1 year)
License MIT + file LICENSE
Depends R (>= 2.14.0), survival
Imports piano, survcomp, reshape2
LinkingTo
Suggests snowfall, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source saps_2.4.2.tar.gz
Windows Binary saps_2.4.2.zip
Mac OS X 10.9 (Mavericks) saps_2.4.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/saps/tree/release-3.3
Package Short Url http://bioconductor.org/packages/saps/
Package Downloads Report Download Stats

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