eaBrowse {EnrichmentBrowser} | R Documentation

## Exploration of enrichment analysis results

### Description

Functions to extract a flat gene set ranking from an enrichment analysis result object and to detailedly explore it.

### Usage

    eaBrowse(
      res,
      nr.show = -1,
      graph.view = NULL,
      html.only = FALSE,
      out.dir = NULL,
      report.name = NULL
    )

    gsRanking(res, signif.only = TRUE)

### Arguments

`res` | Enrichment analysis result list (as returned by the functions `sbea` and `nbea`).
`nr.show` | Number of gene sets to show. As default all statistically significant gene sets are displayed.
`graph.view` | Optional. Should a graph-based summary (reports and visualizes consistency of regulations) be created for the result? If specified, it needs to be a gene regulatory network, i.e. either an absolute file path to a tabular file or a character matrix with exactly *THREE* cols; 1st col = IDs of regulating genes; 2nd col = corresponding regulated genes; 3rd col = regulation effect; Use '+' and '-' for activation/inhibition.
`html.only` | Logical. Should the html file only be written (without opening the browser to view the result page)? Defaults to FALSE.
`out.dir` | Output directory. If `NULL`, defaults to a timestamp-generated subdirectory of `configEBrowser("OUTDIR.DEFAULT")`.
`report.name` | Name of the HTML report. If `NULL`, defaults to the enrichment method used.
`signif.only` | Logical. Display only those gene sets in the ranking, which satisfy the significance level? Defaults to TRUE.

### Value

gsRanking: `DataFrame` with gene sets ranked by the corresponding p-value;

eaBrowse: none, opens the browser to explore results.

If not instructed otherwise (via argument `out.dir`), the main HTML report and associated files are written to `configEBrowser("OUTDIR.DEFAULT")`. See `?configEBrowser` to change the location. If `html.only=FALSE`, the HTML report will automatically be opened in your default browser.

### Author(s)

Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>

### See Also

`sbea`, `nbea`, `combResults`

### Examples

        # real data
        exprs.file <- system.file("extdata/exprs.tab", package="EnrichmentBrowser")
        cdat.file <- system.file("extdata/colData.tab", package="EnrichmentBrowser")
        rdat.file <- system.file("extdata/rowData.tab", package="EnrichmentBrowser")
        probeSE <- readSE(exprs.file, cdat.file, rdat.file)
        geneSE <- probe2gene(probeSE)
        geneSE <- deAna(geneSE)
        metadata(geneSE)$annotation <- "hsa"

        # artificial enrichment analysis results
        gs <- makeExampleData(what="gs", gnames=names(geneSE))
        ea.res <- makeExampleData(what="ea.res", method="ora", se=geneSE, gs=gs)

        # (5) result visualization and exploration
        gsRanking(ea.res)

        out.dir <- configEBrowser("OUTDIR.DEFAULT")
        eaBrowse(ea.res, out.dir=out.dir, report.name="oraReport")

[Package EnrichmentBrowser version 2.22.2 Index]