Survival analysis using transcriptional networks inferred by the RTN package

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Documentation for package ‘RTNsurvival’ version 1.28.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

RTNsurvival-package	Performs survival analysis using transcriptional networks inferred by the RTN package.
hclust_semisupervised	Semi-supervised hierarchical clustering
RTNsurvival	Performs survival analysis using transcriptional networks inferred by the RTN package.
survival.data	A pre-processed dataset for demonstration purposes only.
tni2tnsPreprocess	Preprocessing of TNS class objects
tni2tnsPreprocess-method	Preprocessing of TNS class objects
TNS	TNS: An S4 class for survival analysis using transcriptional networks inferred by the RTN package.
TNS-class	TNS: An S4 class for survival analysis using transcriptional networks inferred by the RTN package.
tnsAREA3	Compute regulon activity by calling aREA (analytic Rank-based Enrichment Analysis) algorithm
tnsAREA3-method	Compute regulon activity by calling aREA (analytic Rank-based Enrichment Analysis) algorithm
tnsCox	Cox regression analysis for TNS class objects
tnsCox-method	Cox regression analysis for TNS class objects
tnsCoxInteraction	Cox regression analysis for dual regulons
tnsCoxInteraction-method	Cox regression analysis for dual regulons
tnsGet	Get information from slots in a TNS object
tnsGet-method	Get information from slots in a TNS object
tnsGSEA2	Compute regulon activity using 2-tailed Gene Set Enrichment Analysis
tnsGSEA2-method	Compute regulon activity using 2-tailed Gene Set Enrichment Analysis
tnsInteraction	Survival analysis for dual regulons
tnsInteraction-method	Survival analysis for dual regulons
tnsKM	Kaplan-Meier analysis for TNS class objects
tnsKM-method	Kaplan-Meier analysis for TNS class objects
tnsKmInteraction	Kaplan-Meier analysis for dual regulons
tnsKmInteraction-method	Kaplan-Meier analysis for dual regulons
tnsPlotCovariates	Plot regulon activity and categorical covariates
tnsPlotCovariates-method	Plot regulon activity and categorical covariates
tnsPlotCox	Cox plots for TNS class objects
tnsPlotCox-method	Cox plots for TNS class objects
tnsPlotCoxInteraction	Plot results from Cox regression analysis for dual regulons
tnsPlotCoxInteraction-method	Plot results from Cox regression analysis for dual regulons
tnsPlotGSEA2	Plot 2-tailed GSEA for a sample from a TNS
tnsPlotGSEA2-method	Plot 2-tailed GSEA for a sample from a TNS
tnsPlotKM	Kaplan-Meier plots for TNS class objects
tnsPlotKM-method	Kaplan-Meier plots for TNS class objects
tnsPlotKmInteraction	Plot results from Kaplan-Meier analysis for dual regulons
tnsPlotKmInteraction-method	Plot results from Kaplan-Meier analysis for dual regulons
tnsPlotSRE	Plot Subgroup Regulon Enrichment for TNS-class objects
tnsPlotSRE-method	Plot Subgroup Regulon Enrichment for TNS-class objects
tnsSRD	Subgroup Regulon Difference for TNS-class objects
tnsSRD-method	Subgroup Regulon Difference for TNS-class objects
tnsSRE	Subgroup Regulon Enrichment for TNS-class objects
tnsSRE-method	Subgroup Regulon Enrichment for TNS-class objects
tnsStratification	Sample stratification for a TNS object