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