tnsPlotCox-methods: Cox plots for TNS class objects

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

Description

Run Cox multivariate regression for regulons and key covariables.

Usage

## S4 method for signature 'TNS'
tnsPlotCox(tns, regs = NULL, fname = "coxplot",
  fpath = ".", ylab = "Regulons and other covariates",
  xlab = "Hazard Ratio (95% CI)", width = 5, height = 5,
  xlim = c(0.3, 3), sortregs = TRUE, plotpdf = FALSE)

Arguments

tns	A TNS object, which must have passed GSEA2 analysis.
regs	An optional string vector specifying regulons to make the plot.
fname	A string. The name of the PDF file which will contain the plot.
fpath	A string. The directory where the file will be saved.
ylab	A string. The label of the y-axis, describing what is represented.
xlab	A string. The label of the x-axis.
width	A numeric value. The width of the plot.
height	A numeric value. The height of the plot.
xlim	A vector with 2 values indicating lowest and highest HR values.
sortregs	A logical value. If TRUE, regulons are sorted from most negatively associated with hazard to most positively associated with hazard.
plotpdf	A logical value.

Value

A Cox hazard model plot and statistics.

Examples

# load survival data
data(survival.data)

# load TNI-object
data(stni, package = "RTN")

stns <- tni2tnsPreprocess(stni, survivalData = survival.data, 
keycovar = c('Age','Grade'), time = 1, event = 2)
stns <- tnsGSEA2(stns)
stns <- tnsCox(stns, regs = c('PTTG1','E2F2','FOXM1'))
tnsPlotCox(stns)

csgroen/RTNsurvival documentation built on May 20, 2019, 1:49 p.m.