tnsGSEA2-methods: Compute regulon activity using 2-tailed Gene Set Enrichment...

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

Description

Works as a wrapper for tni.gsea2, performing a 2-tailed GSEA analysis on a TNI class object and integrating the results into the TNS class object.

Usage

## S4 method for signature 'TNS'
tnsGSEA2(tns, ...)

Arguments

tns	A TNS class, which has been preprocessed
...	Additional parameters passed to tni.gsea2 function.

Value

A TNS class, with added regulon activity scores.

See Also

tni.gsea2 for information on all parameters.

Examples

# load survival data
data(survival.data)

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

stns <- tni2tnsPreprocess(stni, survivalData = survival.data, 
keycovar = c('Grade','Age'), time = 1, event = 2)
stns <- tnsGSEA2(stns)

## Not run: 

# parallel version with SNOW package!
library(snow)
options(cluster=makeCluster(3, "SOCK"))
stns <- tnsGSEA2(stns)
stopCluster(getOption("cluster"))


## End(Not run)

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