tnsCox-methods: Cox regression analysis 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 other covariates.

Usage

## S4 method for signature 'TNS'
tnsCox(tns, regs = NULL, qqkeycovar = FALSE,
  verbose = TRUE)

Arguments

tns	A TNS object, which must have passed GSEA2 analysis.
regs	An optional string vector listing regulons to be tested.
qqkeycovar	A logical value. If TRUE, only the samples in the 2nd and 3rd quartils of 'keycovar' are used in the analysis. If FALSE, all samples are used (see tni2tnsPreprocess).
verbose	A logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

Value

Cox hazard models 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'))
tnsGet(stns, "coxTable")

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