RTNsurvival-package {RTNsurvival} | R Documentation

## Performs 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.

[Package RTNsurvival version 1.12.2 Index]