tnsCoxInteraction-methods: Cox regression analysis for dual regulons

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

Description

Cox regression analysis for dual regulons, including the interaction term.

Usage

## S4 method for signature 'TNS'
tnsCoxInteraction(tns, stepFilter = TRUE,
  pValueCutoff = 0.05, verbose = TRUE)

Arguments

tns	A TNS object with regulons used to compute the dual regulons.
stepFilter	A single logical value specifying to use a step-filter algorithm, testing dual regulons that have at least one significant predictor in the 'tnsCox' method (when stepFilter=TRUE) or not (when stepFilter=FALSE).
pValueCutoff	An numeric value. The p-value cutoff applied to the results from the previous steps of the analysis pipeline (when stepFilter=TRUE).
verbose	A logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

Value

Cox hazard models and statistics.

An updated TNS-class object containing Cox regression models for all given duals

Examples

# load survival data
data(survival.data)

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

# perform survival analysis for regulons
stns <- tni2tnsPreprocess(stni, survivalData = survival.data, 
time = 1, event = 2)
stns <- tnsGSEA2(stns)

# run Cox regression for dual regulons
stns <- tnsCoxInteraction(stns, stepFilter = FALSE)
tnsGet(stns, "coxInteractionTable")

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