RTNsurvival-package: Performs survival analysis using transcriptional networks...

In RTNsurvival: Survival analysis using transcriptional networks inferred by the RTN package

Description

This package provides classes and methods to perform survival analysis using transcriptional networks inferred by the RTN package, including Kaplan-Meier and multivariate survival analysis using Cox's regression model.

Details

Package:	RTNsurvival
Type:	Package
Depends:	R(>= 3.5), RTN(>= 2.6.3), RTNduals(>= 1.6.1), methods
Imports:	survival, RColorBrewer, grDevices, graphics, stats, utils, scales, data.table, egg, ggplot2, pheatmap, dunn.test
Suggests:	Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
License:	Artistic-2.0
biocViews:	NetworkInference, NetworkEnrichment, GeneRegulation, GeneExpression, GraphAndNetwork, GeneSetEnrichment

Index

TNS-class:	an S4 class for survival survival analysis using RTN transcriptional networks.
tni2tnsPreprocess:	a preprocessing method for objects of class TNS.
tnsGSEA2:	compute regulon activity by calling 'GSEA2' algorithm.
tnsPlotGSEA2:	plot results from the two-tailed GSEA.
tnsKM:	Kaplan-Meier analysis for TNS class objects.
tnsPlotKM:	Kaplan-Meier plots for TNS class objects.
tnsCox:	Cox regression analysis for TNS class objects.
tnsPlotCox:	Cox plots for TNS class objects.
tnsGet:	Get information from slots in a TNS object.
tnsInteraction:	A generic call to 'tnsCoxInteraction' and 'tnsKmInteraction'.
tnsKmInteraction:	Kaplan-Meier analysis for dual regulons.
tnsPlotKmInteraction:	Plot results from Kaplan-Meier analysis for dual regulons.
tnsCoxInteraction:	Cox regression analysis for dual regulons.
tnsPlotCoxInteraction:	Plot results from Cox regression analysis for dual regulons.
tnsPlotGSEA2:	Plot 2-tailed GSEA for a sample from a TNS.
tnsAREA3:	compute regulon activity by calling 'aREA3' algorithm.

Further information is available in the vignettes by typing vignette("RTNsurvival"). Documented topics are also available in HTML by typing help.start() and selecting the RTNsurvival package from the menu.

Author(s)

Clarice S. Groeneveld, Vinicius S. Chagas, Gordon Robertson, ..., Kerstin Meyer, Mauro A. A. Castro

References

Fletcher M.N.C. et al., Master regulators of FGFR2 signalling and breast cancer risk. Nature Communications, 4:2464, 2013.

Castro M.A.A. et al., Regulators of genetic risk of breast cancer identified by integrative network analysis. Nature Genetics, 48:12-21, 2016.

RTNsurvival documentation built on Nov. 12, 2020, 2 a.m.