tnsPlotGSEA2,TNS-method {RTNsurvival} | R Documentation

## Plot 2-tailed GSEA for a sample from a TNS

### Description

Makes a 2-tailed GSEA plot for a certain phenotype (sample) present in a TNS. A wrapper of `tna.plot.gsea2`

### Usage

    ## S4 method for signature 'TNS'
    tnsPlotGSEA2(
      tns,
      aSample,
      regs = NULL,
      refsamp = NULL,
      checklog = FALSE,
      ntop = NULL,
      pValueCutoff = 0.05,
      pAdjustMethod = "BH",
      verbose = TRUE,
      plotpdf = FALSE,
      ...
    )

### Arguments

`tns` | A TNS object
`aSample` | A string specifying a given sample number present in the 'survivalData' table.
`regs` | An optional string vector specifying regulons to make the plot.
`refsamp` | A character vector.
`checklog` | A logical value. If TRUE, expression values are transformed into log space.
`ntop` | An optional integer value. The number of regulons for which the GSEA2 will be plotted.
`pValueCutoff` | An numeric value. The p-value cutoff for the analysis.
`pAdjustMethod` | A character. Specifies the adjustment method for the pvalue. See `p.adjust`
`verbose` | A logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).
`plotpdf` | A single logical value.
`...` | parameters which will be passed to `tna.plot.gsea2`, such as ylimPanels, heightPanels, width, height, ylabPanels, xlab...

### Value

A plot containing the 2-tailed GSEA analysis for a phenotype.

### See Also

`tna.plot.gsea2` for all plot 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, verbose=FALSE)
    tnsPlotGSEA2(stns, 'MB-5115', regs = 'FOXM1', plotpdf = FALSE)

[Package RTNsurvival version 1.12.2 Index]