eaBrowse {EnrichmentBrowser} | R Documentation |
Functions to extract a flat gene set ranking from an enrichment analysis result object and to detailedly explore it.
eaBrowse(res, nr.show = -1, graph.view = NULL, html.only = FALSE, out.dir = NULL, report.name = NULL) gsRanking(res, signif.only = TRUE)
res |
Enrichment analysis result list (as returned by the functions
|
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 |
report.name |
Name of the HTML report. If |
signif.only |
Logical. Display only those gene sets in the ranking, which satisfy the significance level? Defaults to TRUE. |
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.
Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>
# 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")