tnsGSEA2,TNS-method {RTNsurvival} | R Documentation

## Compute regulon activity using 2-tailed Gene Set Enrichment Analysis

### 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=snow::makeCluster(3, "SOCK"))
    stns <- tnsGSEA2(stns)
    stopCluster(getOption("cluster"))

    ## End(Not run)

[Package RTNsurvival version 1.11.2 Index]