tnsSRD,TNS-method {RTNsurvival} | R Documentation

## Subgroup Regulon Difference for TNS-class objects

### Description

This regulon evaluates differences between regulon activity of subgroups of samples, given a grouping variable. It performs Wilcoxon-Mann-Whitney (2 subgroups) or Kruskal-Wallis (3+ subgroups) Rank Sum Tests to check whether the activity scores of a given regulon are different between subgroups of samples.

### Usage

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

### 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.
`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).
`regs` | An optional string vector specifying regulons to use for the analysis.
`verbose` | a logical value specifying whether to display messages and progress bar.

### Value

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

### 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 <- tnsSRD(stns, "ER+")

[Package RTNsurvival version 1.12.2 Index]