eaBrowse: Exploration of enrichment analysis results

In lgeistlinger/EnrichmentBrowser: Seamless navigation through combined results of set-based and network-based enrichment analysis

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

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")

lgeistlinger/EnrichmentBrowser documentation built on May 9, 2024, 7:22 p.m.