Significance Analysis of Prognostic Signatures


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Documentation for package ‘saps’ version 2.2.0

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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