Description Usage Arguments Value Author(s) See Also Examples
Functions to extract a flat gene set ranking from an enrichment analysis result object and to detailedly explore it.
1 2 3 4 5 6 7 8 9 10 |
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>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 |
# 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")
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.