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 preranked 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 Qvalue is computed to estimate the significance of the SAPS_score by calculating SAPS_scores for random gene sets.
Package details 


Author  Daniel Schmolze [aut, cre], Andrew Beck [aut], Benjamin HaibeKains [aut] 
Bioconductor views  BiomedicalInformatics DifferentialExpression GeneExpression GeneSetEnrichment Survival 
Maintainer  Daniel Schmolze <saps@schmolze.com> 
License  MIT + file LICENSE 
Version  2.1.0 
Package repository  View on GitHub 
Installation 
Install the latest version of this package by entering the following in R:

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