ea.browse {EnrichmentBrowser} | R Documentation |
Functions to extract a flat gene set ranking from an enrichment analysis result object and to detailedly explore it.
ea.browse( res, nr.show = -1, graph.view = NULL, html.only = FALSE ) gs.ranking( 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. |
signif.only |
Logical. Display only those gene sets in the ranking, which satisfy the significance level? Defaults to TRUE. |
gs.ranking: DataFrame with gene sets ranked by the corresponding p-value;
ea.browse: none, opens the browser to explore results.
Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>
# real data # (1) reading the expression data from file exprs.file <- system.file("extdata/exprs.tab", package="EnrichmentBrowser") pdat.file <- system.file("extdata/colData.tab", package="EnrichmentBrowser") fdat.file <- system.file("extdata/rowData.tab", package="EnrichmentBrowser") probe.eset <- read.eset(exprs.file, pdat.file, fdat.file) gene.eset <- probe.2.gene.eset(probe.eset) gene.eset <- de.ana(gene.eset) metadata(gene.eset)$annotation <- "hsa" # artificial enrichment analysis results gs <- make.example.data(what="gs", gnames=names(gene.eset)) ea.res <- make.example.data(what="ea.res", method="ora", eset=gene.eset, gs=gs) # (5) result visualization and exploration gs.ranking(ea.res) ea.browse(ea.res)