tnsSRE,TNS-method {RTNsurvival} | R Documentation

## Subgroup Regulon Enrichment for TNS-class objects

### Description

This method evaluates which regulons are enriched in sample groups, given a grouping variable. It performs Fisher's Exact Test whether a regulon is positively or negatively enriched in a subgroup using regulon activity.

### Usage

    ## S4 method for signature 'TNS'
    tnsSRE(tns, subgroup, regs = NULL, pValueCutoff = 0.05, pAdjustMethod = "BH")

### Arguments

`tns` | A A TNS object.
`subgroup` | a character vector. It must be the name of a column in the survivalData featuring the grouping information as a categorical variable.
`regs` | An optional string vector specifying regulons to use for the analysis.
`pValueCutoff` | a single numeric value specifying the cutoff for p-values considered significant.
`pAdjustMethod` | a single character value specifying the p-value adjustment method to be used (see 'p.adjust' for details).

### Value

A TNS-class object with the results of the subgroup regulon enrichment added to the results slot. To recover the results, use tnsGet(tns, "regulonEnrichment")

### Examples

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

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

    # run subgroup regulon enrichment analysis
    stns <- tnsSRE(stns, "ER+")

    # plot the result
    tnsPlotSRE(stns)

[Package RTNsurvival version 1.12.2 Index]