saps-package

<code><a href="/link/saps?package=saps&version=2.4.2" rd-options="" data-mini-rdoc="saps::saps">saps</a></code> will usually be the only function needed.

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.

Daniel Schmolze

saps

Significance Analysis of Prognostic Signatures

saps-package function

<code><a href="saps" rd-options="">saps</a></code> will usually be the only function needed.

saps-package: Implements Significance Analysis of Prognostic Signatures (SAPS), a robust method for determining prognostically significant gene sets

Description

Arguments

References